Conformationally stabilized rsv pre-fusion f proteins

ABSTRACT

In some embodiments, the present invention provides respiratory syncytial virus (RSV) F proteins, polypeptides and protein complexes that comprise one or more cross-links to stabilize the protein, polypeptide or protein complex in its pre-fusion conformation. In some embodiments the present invention provides RSV F proteins, polypeptides and protein complexes comprising one or more mutations to facilitate such cross-linking. In some embodiments the present invention provides compositions comprising such proteins, polypeptides or protein complexes, including vaccine compositions, and methods of making and using the same.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional PatentApplication No. 61/858,533, filed Jul. 25, 2013, the contents of whichare hereby incorporated by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under grant number1R43AI112124-01A1 awarded by the National Institute of Allergy andInfectious Diseases (NIAID). The government has certain rights in theinvention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Jul. 24, 2014, isnamed Avatar_(—)007_US2 Sequence Listing.txt and is 195,572 bytes insize.

COPYRIGHT & INCORPORATION-BY-REFERENCE

A portion of the disclosure of this patent document contains materialthat is subject to copyright protection. The copyright owner has noobjection to the facsimile reproduction by anyone of the patent documentor the patent disclosure as it appears in the Patent and TrademarkOffice patent file or records, but otherwise reserves all copyrightrights whatsoever.

For the purposes of only those jurisdictions that permit incorporationby reference, the text of all documents cited herein is herebyincorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

Each year, respiratory syncytial virus (RSV) infects 4-5 millionchildren in the US, and is the leading cause of infant hospitalizations(˜150,000 hospitalizations). Globally, it accounts for 6.7% of deaths ininfants less than 1 year old, second only to malaria. In addition, itposes a serious threat to other high-risk groups, including elderly andimmuno-compromised subjects, where it results in approximately anadditional 180,000 hospitalizations and 12,000 deaths in the US. Thereare no current frontline treatments for RSV, and the only currentlyapproved prophylactic treatment for RSV is passive administration of thelicensed monoclonal antibody Synagis (palivizumab), which recognizes theRSV fusion (F) protein, and reduces incidence of severe disease by only˜50%. The high cost of prophylaxis with Synagis limits its use only topremature infants and infants less than 24 months old with congenitalheart disease. For a review see Costello et al., “Targeting RSV withVaccines and Small Molecule Drugs, Infectious Disorders,” Drug Targets,2012, vol. 12, no. 2. The development of a more effective and, ideally,more cost-effective RSV vaccine would be of enormous value. Clinicalevidence that RSV F protein-specific antibodies can protect againstdisease has prompted a concerted effort to identify additional andbetter monoclonal antibodies, and to develop a protective vaccine toaddress this significant unmet medical need.

BRIEF SUMMARY OF THE INVENTION

Some aspects of the present invention are summarized below. Additionalaspects are described in the Detailed Description of the Invention, theExamples, the Figures and the claims herein.

The RSV F protein is known to induce potent neutralizing antibodies thatcorrelate with protection against RSV. Recently it has been shown thatthe pre-fusion conformation of the RSV F protein trimer (which may bereferred to as “pre-fusion F” or “pre-F” herein) is the primarydeterminant of neutralizing activity in human sera. Also, the mostpotent neutralizing antibodies (nAbs) isolated to date specifically bindonly to the pre-fusion conformation. However, soluble pre-F is highlyunstable and readily transitions to the post-fusionconformation—limiting its usefulness as a vaccine immunogen. An RSV Fprotein stabilized in its pre-fusion (pre-F) conformation could be veryvaluable—providing a candidate RSV vaccine immunogen. Similarly, such astabilized RSV pre-F protein could also be useful for the generation ofantibodies, such as diagnostic and therapeutic antibodies. The crystalstructure of the RSV F protein (bound to a potent nAb—D25) in itspre-fusion conformation was recently described. See McLellan et al.,2013, Science, 340, p. 1113-1117, the contents of which are herebyincorporated by reference in their entirety. Building on this work, thepresent inventors have performed extensive analysis of the structure ofthe RSV F protein and have developed a variety of novel designstrategies and novel constructs to stabilize or “lock” the RSV F proteinin its pre-F conformation.

In some embodiments the present invention provides RSV F polypeptides,proteins, and protein complexes, such as those that can be or arestabilized or “locked” in a pre-fusion conformation, for example usingtargeted cross-links, such as targeted di-tyrosine cross-links. Thepresent invention also provides methods for making and using such RSV Fpolypeptides, proteins, and protein complexes.

In some embodiments, the present invention provides specific locationswithin the amino acid sequence of the RSV F protein at which, or betweenwhich, cross-links can be made in order to stabilize the RSV F proteinin its pre-F conformation. In some embodiments, the cross-links aretargeted di-tyrosine cross-links. Where di-tyrosine cross-links areused, the present invention provides specific amino acid residues (orpairs of amino acid residues) that either comprise a pre-existingtyrosine residue or can be or are mutated to a tyrosine residue suchthat di-tyrosine cross-links can be made.

In some embodiments, the present invention provides an isolated RSV Fpolypeptide, protein or protein complex comprising at least onedi-tyrosine cross-link, wherein at least one tyrosine of the at leastone di-tyrosine cross-links originates from a point mutation totyrosine.

In some embodiments, the invention provides an isolated RSV Fpolypeptide, protein or protein complex having at least about 75%sequence identity to SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, or aminoacid residues 1-513 thereof (comprising the RSV F ectodomain), whereinthe protein polypeptide comprises at least one tyrosine residue thatoriginates from a point mutation to tyrosine. In some such embodimentsthe RSV F polypeptides, proteins or protein complexes contain at leastone di-tyrosine cross-link wherein at least one tyrosine residue of theat least one cross-link originates from a point mutation to tyrosine.

In some embodiments, the invention provides an isolated RSV Fpolypeptide having the amino acid sequence of SEQ ID NO:11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 or32, or amino acid residues 1-513 thereof (comprising the RSV Fectodomain). In some embodiments, the invention provides an isolated RSVF protein or polypeptide having at least about 75% sequence identity toSEQ ID NO:11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31 or 32, or amino acid residues 1-513 thereof(comprising the RSV F ectodomain). In some such embodiments the RSV Fpolypeptides, proteins or protein complexes contain at least onedi-tyrosine cross-link wherein at least one tyrosine residue of the atleast one cross-link originates from a point mutation to tyrosine.

In some embodiments, where di-tyrosine cross-links are present, thedi-tyrosine cross-link comprises two pre-existing tyrosine residues. Insome embodiments, the di-tyrosine cross-link comprises a pre-existingtyrosine cross-linked to a tyrosine originating from a point mutation totyrosine. In some embodiments, the di-tyrosine cross-link comprises twotyrosines originating from point mutations to tyrosine. In someembodiments, the di-tyrosine cross-link comprises an intra-protomerbond, an inter-protomer bond, an intra-molecular bond, aninter-molecular bond, or any combination thereof. In some embodiments,the di-tyrosine cross-link comprises a bond within or between a RSV Fprotein F1 polypeptide and a RSV F protein F2 polypeptide. In someembodiments, the point mutation to tyrosine is located at one or moreamino acid positions selected from the group consisting of amino acidpositions: 77, 88, 97, 147, 150, 155, 159, 183, 185, 187, 220, 222, 223,226, 255, 427 or 469 of SEQ ID NO: 1 or SEQ ID NO: 4, or any amino acidposition that corresponds to one of such amino acid positions in anotherRSV F amino acid sequence or ectodomain thereof.

In some embodiments, the invention provides an isolated RSV Fpolypeptide, protein or protein complex having at least about 75%sequence identity to SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, whereinthe polypeptide comprises at least one di-tyrosine cross-link, whereinone or both tyrosines of the cross-link originates from a point mutationto tyrosine, and wherein the cross-links are located between one or morepaired tyrosine amino acid residues located at amino acid positions: 147and 286; 198 and 220; 198 and 222; 198 and 223; 198 and 226; 33 and 469;77 and 222; 88 and 255; 97 and 159; 183 and 427; 185 and 427; or 187 and427. In some embodiments, the RSV F polypeptide, protein, or proteincomplex comprises more than one di-tyrosine cross-link. In someembodiments, the RSV F polypeptide, protein, or protein complexcomprises two, three, four, five or more di-tyrosine cross-links. Insome embodiments, the RSV F polypeptide, protein, or protein complexcomprises di-tyrosine cross-links at paired tyrosine amino acid residueslocated at amino acid positions 77 and 222, and 33 and 469.

In some embodiments, the RSV F polypeptides, proteins, or proteincomplexes of the invention further comprise one or more additionalcross-links, such as disulfide bonds. In such embodiments, at least onecysteine of the one or more disulfide bonds originates from a pointmutation to cysteine. In some embodiments, the RSV F polypeptides,proteins, or protein complexes further comprise cavity-fillinghydrophobic amino acid substitutions. In some embodiments, the RSV Fpolypeptides, proteins, or protein complexes further comprises atrimerization domain. In such embodiments, the trimerization domain is afoldon domain.

In some embodiments, the RSV F polypeptides, proteins, or proteincomplexes of the invention are capable of eliciting a protective immuneresponse in a subject and/or eliciting production of RSV-specificneutralizing antibodies in a subject. In some embodiments, the RSV Fpolypeptides, proteins, or protein complexes of the invention compriseat least one antigenic site capable of binding a neutralizing antibody,for example, the antigenic site ø.

In some embodiments, the invention provides compositions (such aspharmaceutical compositions and/or vaccine compositions) comprising oneor more RSV F polypeptides, proteins, or protein complexes of theinvention. In some embodiments, such compositions comprise an adjuvant,a carrier, an immunostimulatory agent, or any combination thereof. Insome embodiments, the composition is, or forms part of, a vaccine forrespiratory syncytial virus. In some embodiments, the invention providesa method of vaccinating a subject against RSV, the method comprisingadministering an effective amount of a composition comprising one ormore of the RSV F polypeptides, proteins, or protein complexes of theinvention to a subject. In some embodiments, the subject is a human ofless than 24 months in age or a human of greater than 50 years in age.In some embodiments, the administering comprises a single immunization.In some embodiments, a method of the invention further comprisesadministering to a subject a pharmaceutical composition comprising oneor more RSV F polypeptides, proteins, or protein complexes of theinvention so as to treat or prevent an RSV infection in the subject. Insome embodiments, the invention provides a medicament for inducing animmune response in a subject, comprising one or more the RSV Fpolypeptides, proteins, or protein complexes of the invention. In someembodiments, the medicament is a vaccine.

In some embodiments, the invention provides a method of making a RSVvaccine immunogen, comprising (a) identifying or obtaining a RSV Fpolypeptide, protein or protein complex in a pre-fusion conformation;(b) selecting one or more regions in the RSV F polypeptide, protein orprotein complex where the introduction of one or more cross-links (suchas di-tyrosine cross-links) could stabilize the pre-fusion conformation;(c) introducing into the RSV F protein one or more cross-links (such asdi-tyrosine cross-links) at one or more of the regions selected in step(b) to form an engineered RSV F polypeptide, protein or protein complex;and (d) determining if the engineered RSV F polypeptide, protein orprotein complex has one or more properties selected from the groupconsisting of: (i) enhanced ability bind to a neutralizing antibody,(ii) enhanced ability bind to a broadly neutralizing, (iii) enhancedability bind to and activate B cell receptors, (iv) enhanced ability toelicit an antibody response in an animal, (v) enhanced ability to elicita protective antibody response in an animal, (vi) enhanced ability toelicit production of neutralizing antibodies in an animal, (vii)enhanced ability to elicit production of broadly neutralizing antibodiesin an animal, (viii) enhanced ability to elicit a protective immuneresponse in an animal, and (ix) enhanced ability to bind to and elicitproduction of antibodies that recognize quaternary neutralizing epitopesin an animal, wherein if the engineered RSV F polypeptide, protein orprotein complex has one or more properties i. to ix., the engineered RSVF polypeptide, protein or protein complex is a RSV vaccine immunogencandidate. In some such embodiments, step (d) comprises performing oneor more assays to assess the ability of the engineered RSV F protein tobind to a neutralizing antibody, bind to a broadly neutralizingantibody, bind to and activate a B cell receptors elicit an antibodyresponse in an animal, elicit a protective antibody response in ananimal, elicit production of neutralizing antibodies in an animal,elicit production of broadly neutralizing antibodies in an animal,elicit a protective immune response in an animal, and/or elicitproduction of antibodies that recognize quaternary neutralizing epitopesin an animal. In some embodiments, where di-tyrosine cross-links areused, at least one tyrosine of the one or more di-tyrosine cross-linksintroduced in step (c) originates from a point mutation to tyrosine. Insome embodiments, the method further comprises, prior to step (c),introducing into the RSV F protein one or more point mutations totyrosine at one or more of the regions selected in step (b).

These and other embodiments of the present invention are describedthroughout the present patent specification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B. Amino acid sequences of (A) soluble RSV F protein from RSVsubtype A (WT) (SEQ ID NO:1), and (B) full-length RSV F protein from RSVsubtype A (SEQ ID NO:2) (Accession No. AHJ60043.1). Amino acid residues1-513 of both sequences are the core sequences of the RSV F protein thatare common to both the soluble and membrane-bound (full-length) forms.The C-terminal sequences from amino acid residue 514 onwards in SEQ IDNO. 1 comprise a foldon trimerization domain followed by a thrombincleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag. TheC-terminal sequences from amino acid residue 514 onwards in SEQ ID NO. 2comprise the endogenous RSV F protein sequence containing thetransmembrane region and cytoplasmic tail.

FIGS. 2A-2B. Amino acid sequences of (A) soluble RSV F protein from RSVsubtype B (SEQ ID NO:3), and (B) full-length RSV F protein from RSVsubtype B (SEQ ID NO:4) (Accession No. AHL84194). Amino acid residues1-513 of both sequences are the core sequences of the RSV F protein thatare common to both the soluble and membrane-bound (full-length) forms.The C-terminal sequences from amino acid residue 514 onwards in SEQ IDNO. 3 comprise a foldon trimerization domain followed by a thrombincleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag. TheC-terminal sequences from amino acid residue 514 onwards in SEQ ID NO. 4comprise the endogenous RSV F protein sequence containing thetransmembrane region and cytoplasmic tail.

FIGS. 3A-3B. Amino acid sequences of (A) soluble DS-Cav1 modified RSV Fprotein (SEQ ID NO:5), and (B) full-length DS-Cav1 modified RSV Fprotein (SEQ ID NO:6) (McLellan et al. (2013) Science 342:592-598).Amino acid residues 1-513 of both sequences are the core sequences ofthe RSV F protein that are common to both the soluble and membrane-bound(full-length) forms. The C-terminal sequences from amino acid residue514 onwards in SEQ ID NO. 5 comprise a foldon trimerization domainfollowed by a thrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and astrep tag. The C-terminal sequences from amino acid residue 514 onwardsin SEQ ID NO. 6 comprise the endogenous RSV F protein sequencecontaining the transmembrane region and cytoplasmic tail.

FIGS. 4A-4B. Amino acid sequences of (A) soluble Cav1 modified RSV Fprotein (SEQ ID NO:7), and (B) full-length Cav1 modified RSV F proteinsequence (SEQ ID NO:8) (McLellan et al. (2013) Science 342:592-598).).Amino acid residues 1-513 of both sequences are the core sequences ofthe RSV F protein that are common to both the soluble and membrane-bound(full-length) forms. The C-terminal sequences from amino acid residue514 onwards in SEQ ID NO. 7 comprise a foldon trimerization domainfollowed by a thrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and astrep tag. The C-terminal sequences from amino acid residue 514 onwardsin SEQ ID NO. 8 comprise the endogenous RSV F protein sequencecontaining the transmembrane region and cytoplasmic tail.

FIGS. 5A-5B. Amino acid sequences of (A) soluble DS modified RSV Fprotein (SEQ ID NO:9), and (B) full-length DS modified RSV F proteinsequence (SEQ ID NO:10) (McLellan et al. (2013) Science 342:592-598).).Amino acid residues 1-513 of both sequences are the core sequences ofthe RSV F protein that are common to both the soluble and membrane-bound(full-length) forms. The C-terminal sequences from amino acid residue514 onwards in SEQ ID NO. 9 comprise a foldon trimerization domainfollowed by a thrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and astrep tag. The C-terminal sequences from amino acid residue 514 onwardsin SEQ ID NO. 10 comprise the endogenous RSV F protein sequencecontaining the transmembrane region and cytoplasmic tail.

FIG. 6. Sequence alignment of RSV F proteins from RSV subtype A (SEQ IDNO:1—identified as “RSV_F_WT” in the figure) and subtype B (SEQ IDNO:4). Amino acid residues shown in bold and underlined in the subtype Asequence indicate sites that can be targeted for di-tyrosinecross-linking either as single or double mutants. The equivalent sitesin subtype B are also shown in boxes. The designated positions targetedfor di-tyrosine cross-linking are 100% conserved between RSV subtypes Aand B. Amino acid residues 1-513 of both sequences are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards in SEQ ID NO. 1 comprise a foldon trimerizationdomain followed by a thrombin cleavage site, 6× His-tag (SEQ ID NO: 46),and a strep tag. The C-terminal sequences from amino acid residue 514onwards in SEQ ID NO. 4 comprise the endogenous RSV F protein sequencecontaining the transmembrane region and cytoplasmic tail.

FIG. 7. Sequence alignment of DS-Cav1 RSV F protein (SEQ ID NO:5), andRSV F proteins from RSV subtype A (SEQ ID NO:1) and subtype B (SEQ IDNO:4). The C-terminal sequences shown in italics in the DS-Cav1 and RSVsubtype A sequences (residues 514-568) contain the exogenous Foldontrimerization domain followed by a thrombin cleavage site, 6× His-tag(SEQ ID NO: 46) and a strep tag. The C-terminal sequence shown in boldand underlined in the RSV subtype B sequence (residues 514-574) is theendogenous F protein sequence containing the transmembrane region andcytoplasmic tail.

FIG. 8. Amino acid sequence of a modified soluble RSV F protein (subtypeA) comprising a to-tyrosine mutation at position 147 (A147Y) (SEQ IDNO:11). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 9. Amino acid sequence of a modified soluble RSV F protein (subtypeA) comprising a to-tyrosine mutation at position 220 (V220Y) (SEQ IDNO:12). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 10. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising a to-tyrosine mutation at position 222 (E222Y)(SEQ ID NO:13). Amino acid residues 1-513 are the core sequences of theRSV F protein. The C-terminal sequences from amino acid residue 514onwards comprise a foldon trimerization domain followed by a thrombincleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 11. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising a to-tyrosine mutation at position 223 (F223Y)(SEQ ID NO:14). Amino acid residues 1-513 are the core sequences of theRSV F protein. The C-terminal sequences from amino acid residue 514onwards comprise a foldon trimerization domain followed by a thrombincleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 12. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising a to-tyrosine mutation at position 226 (K226Y)(SEQ ID NO:15). Amino acid residues 1-513 are the core sequences of theRSV F protein. The C-terminal sequences from amino acid residue 514onwards comprise a foldon trimerization domain followed by a thrombincleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 13. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising a to-tyrosine mutation at position 469 (V469Y)(SEQ ID NO:16). Amino acid residues 1-513 are the core sequences of theRSV F protein. The C-terminal sequences from amino acid residue 514onwards comprise a foldon trimerization domain followed by a thrombincleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 14. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 77 (K77Y) and222 (E222Y) (SEQ ID NO:17). Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 15. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 88 (N88Y) and255 (S255Y) (SEQ ID NO:18). Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 16. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 97 (M97Y) and159 (H159Y) (SEQ ID NO:19). Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 17. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 185 (V185Y)and 427 (K427Y) (SEQ ID NO:20). Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 18. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 187 (V187Y)and 427 (K427Y) (SEQ ID NO:21). Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 19. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to tyrosine mutations at positions 183 (N183Y)and 427 (K427Y) (SEQ ID NO:22). Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 20A-20C. Sequence alignment of soluble RSV F protein subtype A (SEQID NO:1) and examples of modified RSV F proteins derived therefrom (SEQID NOS:11-21) comprising single or double to-tyrosine mutations.Tyrosines in boxes are introduced into the WT subtype A sequence. Wheretwo new tyrosines are introduced into the same sequence, they aretypically intended to cross-link with each other. Where only a singletyrosine is introduced, that tyrosine is typically expected tocross-link with an endogenous or pre-existing tyrosine in that sequencewhich is shown in bold and underlined. Amino acid residues 1-513 of eachsequence are the core sequences of the RSV F protein. The C-terminalsequences from amino acid residue 514 onwards comprise a foldontrimerization domain followed by a thrombin cleavage site, 6× His-tag(SEQ ID NO: 46), and a strep tag.

FIG. 21. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising a to-tyrosine mutation at position 147 (A147Y) (SEQID NO:23). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 22. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising a to-tyrosine mutation at position 220 (V220Y) (SEQID NO:24). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 23. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising a to-tyrosine mutation at position 222 (E222Y) (SEQID NO:25). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 24. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising a to-tyrosine mutation at position 223 (F223Y) (SEQID NO:26). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 25. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising a to-tyrosine mutation at position 226 (K226Y) (SEQID NO:27). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 26. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising a to-tyrosine mutation at position 469 (V469Y) (SEQID NO:28). Amino acid residues 1-513 are the core sequences of the RSV Fprotein. The C-terminal sequences from amino acid residue 514 onwardscomprise a foldon trimerization domain followed by a thrombin cleavagesite, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 27. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 222 (E222Y)and 469 (V469Y) (SEQ ID NO:29) designed to facilitate the formation ofmultiple di-tyrosine cross-links. Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 28. Amino acid sequence of a modified soluble RSV F protein(subtype A) comprising to-tyrosine mutations at positions 226 (K226Y)and 469 (V469Y) (SEQ ID NO:30) designed to facilitate the formation ofmultiple di-tyrosine cross-links. Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 29. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising to-tyrosine mutations at positions 222 (E222Y) and469 (V469Y) (SEQ ID NO:31) designed to facilitate the formation ofmultiple di-tyrosine cross-links. Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIG. 30. Amino acid sequence of a modified soluble RSV F protein(DS-Cav1) comprising to-tyrosine mutations at positions 226 (K226Y) and469 (V469Y) (SEQ ID NO:32) designed to facilitate the formation ofmultiple di-tyrosine cross-links. Amino acid residues 1-513 are the coresequences of the RSV F protein. The C-terminal sequences from amino acidresidue 514 onwards comprise a foldon trimerization domain followed by athrombin cleavage site, 6× His-tag (SEQ ID NO: 46), and a strep tag.

FIGS. 31A-31B. Ribbon diagrams depicting examples of two targetedpositions in the RSV prefusion F protein trimer where intra-protomericand intra-protomeric di-tyrosine cross-links can be introduced. (A)Side-view (and enlargement) of an engineered F1-F1 inter-protomericdi-tyrosine bond between a tyrosine introduced at position 185 (V185Y)and a tyrosine introduced at position 427 (K427Y) (SEQ ID NO:20). (B)Top-down view (and enlargement) of an engineered F1-F1 intra-protomericdi-tyrosine bond between an endogenous tyrosine at position 198 (198Y)and a tyrosine introduced at position 222 (E222Y) (SEQ ID NO:13).Targeted tyrosine residues are depicted in square boxes.

FIG. 32. Alignment of the RSV typeAF protein sequence (SEQ ID NO: 47),and of the prefusion and post-fusion secondary structures. Cylinders andarrows below the sequence represent α-helices and β-strands,respectively. An “X” below the amino acid sequence indicates where thestructure is disordered or missing. Gray shadowing indicates theposition of residues that move more than 5 Å in the transition from theprefusion to postfusion conformation. Black triangles indicate sites ofN-linked glycosylation, text and lines above the amino acid sequenceindicate the antigenic sites, and arrows indicate the position of thefurin cleavage sites. Figure from McLellan et al., 2013, Science340:1113-1117, supplementary materials.

FIG. 33. Illustrative nucleic acid construct for expression of RSV Fprotein in mammalian cells.

FIG. 34. Targeted di-tyrosine cross-linking of RSV F protein. HEK 293cells were transfected with vectors expressing RSV-F variants thatenabling F₁-F₁ intra-protomer DT-cross-links (E222Y (SEQ ID NO: 13) andK226Y (SEQ ID NO:15)), F₁-F₂ intra-protomer DT-cross-links (V469Y (SEQID NO:16) and N88Y-S255Y (SEQ ID NO:18)), or F₁-F₁ intermolecularDT-cross-links (V185Y-K427Y (SEQ ID NO:20)). Background-subtractedfluorescence intensity values are shown. (INT) intensity, (DT)di-tyrosine, (−) and (+) indicate before and after application of thedi-tyrosine cross-linking technology, respectively.

FIGS. 35A-35B. Di-tyrosine cross-linking stabilizes key epitope on RSVprefusion F protein. HEK 293 cells were transfected with constructsexpressing the wild-type (WT) RSV-F or a variant containing the K226Ysubstitution. (A) 72 h post transfection, supernatents were cross-linked(DT) or left uncross-linked and total protein was measured by ELISAusing a high-affinity human anti-hRSV antibody (100 ng/ml in PBS) thatrecognizes both pre- and post-fusion forms of RSV-F. (B) Followingstorage at 4 degrees C. for 16 days presentation of site ø was measuredby ELISA using a preF specific human monoclonal antibody (2 μg/ml inPBS) that recognizes site ø.

FIGS. 36A-36B. Sequence alignment of nucleotide sequences encoding theRSV F protein (full-length—with transmembrane and cytoplasmic domains)from RSV subtype A (SEQ ID NO:33—as “RSV_F_WT_Subtype_A” in the figure)and RSV subtype B (SEQ ID NO:34—identified as “RSV_F_WT_Subtype_B” inthe figure). Nucleotides 1-1539 encode amino acid residues 1-513, whichare the core ectodomain sequences of the RSV F protein. Nucleotides 1540onwards comprise sequences that encode the endogenous RSV Ftransmembrane region and cytoplasmic tail.

FIG. 37. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in human cells(SEQ ID NO:35). Nucleotides 1-1539 encode amino acid residues 1-513,which are the core ectodomain sequences of the RSV F protein.Nucleotides 1540 onwards comprise sequences that encode the endogenousRSV F transmembrane region and cytoplasmic tail.

FIG. 38. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in hamster cells(such as CHO cells) (SEQ ID NO:36). Nucleotides 1-1539 encode amino acidresidues 1-513, which are the core ectodomain sequences of the RSV Fprotein. Nucleotides 1540 onwards comprise sequences that encode theendogenous RSV F transmembrane region and cytoplasmic tail.

FIG. 39. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in insect cells(such as SF9 insect cells) (SEQ ID NO:37). Nucleotides 1-1539 encodeamino acid residues 1-513, which are the core ectodomain sequences ofthe RSV F protein. Nucleotides 1540 onwards comprise sequences thatencode the endogenous RSV F transmembrane region and cytoplasmic tail.

FIG. 40. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in mouse cells(SEQ ID NO:38). Nucleotides 1-1539 encode amino acid residues 1-513,which are the core ectodomain sequences of the RSV F protein.Nucleotides 1540 onwards comprise sequences that encode the endogenousRSV F transmembrane region and cytoplasmic tail.

FIG. 41. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype B that has been codon optimized for expression in human cells(SEQ ID NO:39). Nucleotides 1-1539 encode amino acid residues 1-513,which are the core ectodomain sequences of the RSV F protein.Nucleotides 1540 onwards comprise sequences that encode the endogenousRSV F transmembrane region and cytoplasmic tail.

FIG. 42. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype B that has been codon optimized for expression in hamster cells(such as CHO cells) (SEQ ID NO:40). Nucleotides 1-1539 encode amino acidresidues 1-513, which are the core ectodomain sequences of the RSV Fprotein. Nucleotides 1540 onwards comprise sequences that encode theendogenous RSV F transmembrane region and cytoplasmic tail.

FIG. 43. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype B that has been codon optimized for expression in insect cells(such as SF9 insect cells) (SEQ ID NO:41). Nucleotides 1-1539 encodeamino acid residues 1-513, which are the core ectodomain sequences ofthe RSV F protein. Nucleotides 1540 onwards comprise sequences thatencode the endogenous RSV F transmembrane region and cytoplasmic tail.

FIG. 44. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype B that has been codon optimized for expression in mouse cells(SEQ ID NO:42). Nucleotides 1-1539 encode amino acid residues 1-513,which are the core ectodomain sequences of the RSV F protein.Nucleotides 1540 onwards comprise sequences that encode the endogenousRSV F transmembrane region and cytoplasmic tail.

FIG. 45. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in human cellsand also comprises DS-CAV1 mutations (SEQ ID NO:43). The mutations areshown in bold and with boxes surrounding the mutated codons. Nucleotides1-1539 encode amino acid residues 1-513, which are the core ectodomainsequences of the RSV F protein. Nucleotides 1540 onwards comprisesequences that encode the endogenous RSV F transmembrane region andcytoplasmic tail.

FIG. 46. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in human cellsand also comprises DS mutations (SEQ ID NO:44). The mutations are shownin bold and with boxes surrounding the mutated codons. Nucleotides1-1539 encode amino acid residues 1-513, which are the core ectodomainsequences of the RSV F protein. Nucleotides 1540 onwards comprisesequences that encode the endogenous RSV F transmembrane region andcytoplasmic tail.

FIG. 47. Nucleotide sequences encoding the RSV F protein(full-length—with transmembrane and cytoplasmic domains) from RSVsubtype A that has been codon optimized for expression in human cellsand also comprises CAV1 mutations (SEQ ID NO:45). The mutations areshown in bold and with boxes surrounding the mutated codons. Nucleotides1-1539 encode amino acid residues 1-513, which are the core ectodomainsequences of the RSV F protein. Nucleotides 1540 onwards comprisesequences that encode the endogenous RSV F transmembrane region andcytoplasmic tail.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides, in part, RSV F polypeptides, proteinsand protein complexes, such as those that can be or are stabilized in apre-fusion conformation, methods of making such polypeptides, proteinsand protein complexes, compositions (such as pharmaceutical compositionsand vaccine compositions) comprising such polypeptides, proteins andprotein complexes, and methods of use of such polypeptides, proteins andprotein complexes, for example in vaccination methods, therapeuticmethods and other methods. In some embodiments, the RSV polypeptides,proteins and protein complexes may be useful asconformationally-specific immunogens, for example in RSV vaccines.

DEFINITIONS AND ABBREVIATIONS

As used in the present specification the terms “about” and“approximately,” when used in relation to numerical values, meanwithin + or −20% of the stated value.

As used herein the terms “protein” and “polypeptide” are usedinterchangeably, unless otherwise stated. As used herein the term“protein complex” refers to an assembly of two or more proteins orprotein subunits, such as two or more monomers or protomers. Unlessotherwise stated, all description herein that relates to proteinsapplies equally to protein complexes, and vice versa.

As used herein the terms “stabilized” and “locked” are usedinterchangeably, for example in relation to the effect of cross-linkingin stabilizing or locking the RSV F protein in its pre-fusionconformation. These terms do not require 100% stability. Rather theseterms denote a degree of improved or increased stability. For example,in some embodiments, when the term “stabilized” is used in relation to aRSV F protein cross-linked in its pre-fusion conformation, the termdenotes that the pre-fusion conformation has greater stability than itwould have had prior to or without such cross-linking. Stability, andrelative stability, may be measured in various ways as described inother sections of this application, for example based on the half-lifeof the RSV pre-fusion conformation. The improvement or increase instability may be to any degree that is useful or significant for theintended application. For example, in some embodiments stability may beincreased by about 10%, 25%, 50%, 100%, 200% (i.e. 2-fold), 300% (i.e.3-fold), 400% (i.e. 4-fold), 500% (i.e. 5-fold), 1000% (i.e. 10-fold),or more.

RSV F Polypeptides, Proteins & Protein Complexes

The RSV Fusion or “F” protein is the envelope glycoprotein ofrespiratory syncytial viruses. The RSV F protein may be translated as asingle polypeptide precursor in either a soluble (without thetransmembrane domain) or membrane-bound (with the transmembrane domain)form. This polypeptide forms a trimer, which may, in some situations, beproteolytically cleaved by one or more cellular proteases at conservedfurin consensus cleavage sites to yield two disulfide-bonded fragmentsknown as the F1 (C-terminal) and F2 (N-terminal) fragments. The F2fragment includes approximately the first 83 amimo acids of the RSV Fprecursor. Either the uncleaved precursor protein, or a heterodimer ofthe cleaved F2 and F1 fragments, can form an RSV F protomer. Three suchprotomers assemble to form the final RSV F protein complex, which is ahomotrimer of three protomers.

The RSV F protein trimer mediates fusion of viral and cellularmembranes. The pre-fusion conformation of the RSV F protein trimer(which may be referred to herein as “pre-F”) is highly unstable(metastable). However, once the RSV virus docks with the cell membrane,the RSV F protein trimer undergoes a series of conformational changesand transitions to a highly stable post-fusion (“post-F”) conformation.The RSV F protein is known to induce potent neutralizing antibodies(nAbs) that correlate with RSV protection. For example, immunizationwith the RSV F protein induces nAbs that are protective in humans (e.g.Synagis). Several neutralizing epitopes (sites I, II and IV) are presenton the post-fusion form of RSV F protein. Recently, however, Magro etal. showed that incubation of human sera with the RSV F protein in itspost-fusion conformation failed to deplete the majority of neutralizingactivity against the F protein, indicating the presence of neutralizingantigenic sites unique to the pre-fusion conformation (Magro et al.2012, PNAS 109(8): 3089). By x-ray crystallography, the epitopesrecognized by palivizumab (Synagis), motavizumab (Numax), and that ofthe more recently discovered 101F monoclonal antibody (McLellan et al.,2010, J. Virol., 84(23): 12236-441; and McLellan et al., 2010, Nat.Struct. Mol. Biol., February 17(2): 248-50) were mapped. Most recently,McLellan et al. (Science 340:1113-1117 (2013)) solved the structure ofthe F protein in its pre-fusion conformation, which revealed a novelneutralizing epitope—site ø—that is only displayed in the pre-fusionconformation, and to which a series of antibodies bind, e.g. 5C4, thatare up to 50-fold more potently neutralizing than Synagis and Numax.Accordingly, there is mounting evidence that an RSV vaccine immunogen inthis pre-fusion conformation and displaying site ø could eliciteffective protection. However, to date the highly unstable (metastable)nature of the pre-fusion conformation of the RSV F protein has proved tobe a significant barrier to the development of such a vaccine. Based ona comparison of the pre- and post-fusion RSV F structures of McLellan etal. there appear to be two regions of the F protein that undergo largeconformational changes (>5 Å). These regions are located at the N- andC-termini of the F1 subunit (residues 137-216 and 461-513, respectively)(see FIG. 32). In the crystal structure of the RSV F protein held in itspre-fusion conformation by the D25-antibody bound to the site ø epitope,the C-terminal F1 residues can be stabilized in the pre-fusionconformation by appending a foldon trimerization domain. To stabilizethe N-terminal region of F1, McLellan et al. found that binding of theantibody D25 was sufficient for crystallographic studies. However, forproduction of a vaccine immunogen alternative stabilization strategiesare needed, such as those that do not require the RSV F protein to bebound to a large antibody molecule. One alternative approach that hasbeen attempted involved the introduction of paired cysteine mutations(for disulfide bond formation) and cavity-filling mutations near the F1N-terminus (see the DS-Cav1 RSV F protein variant described in McLellanet al. (2013) Science 342:592-598, which is hereby incorporated byreference in its entirety). However, crystallographic analysis of suchvariants revealed that the structure was only partially in thepre-fusion conformation. Accordingly, additional engineering of the RSVF protein is needed in order to achieve an immunogen for clinicalvaccine development.

The present invention provides certain alternative approaches forstabilizing the RSV F protein in its pre-fusion conformation, includingproviding specific locations within the RSV F protein that can be orshould be cross-linked, and providing mutant forms of the RSV F proteinthat can facilitate the formation of such cross-links. Such cross-linksand mutations can be used alone (e.g. in the context of a wild type RSVF protein or in the context of a RSV F protein that does not compriseany man made mutations or other man made modifications), or can be usedin combination with one or more other man made mutations, modifications,cross-links, or stabilization strategies. Thus, for example, theapproaches described herein can be used in conjunction with the use ofadded foldon trimerization domains, stabilizing antibodies (such asD25), and/or other partially or potentially stabilizing modifications ormutations—such as those in the DS-Cav1 RSV F protein variant describedby McLellan et al.

The present inventors have performed extensive analysis of the structureof the RSV F protein and have developed a variety of novel designstrategies and novel engineered RSV F polypeptides, proteins and proteincomplexes. The present invention also provides methods for making andusing such RSV F polypeptides, proteins, and protein complexes. In someembodiments, the present invention provides specific locations withinthe amino acid sequence of the RSV F protein at which, or between which,targeted cross-links can be made in order to “lock” the RSV F protein inits pre-F conformation. In some embodiments, the targeted cross-linksare di-tyrosine cross-links. Where di-tyrosine cross-links are used, thepresent invention provides specific amino acid residues (or pairs ofamino acid residues) that either comprise a pre-existing tyrosineresidue or can be or are mutated to a tyrosine residue such thatdi-tyrosine cross-links can be made.

Throughout the present patent specification, when reference is made tospecific amino acid residues or specific amino acid regions in the RSV Fprotein by referring to their amino residue number or numbers (such asamino acid residues 77, 88, 97, or 222, for example), and unlessotherwise stated, the numbering is based on the RSV amino acid sequencesprovided herein in the sequence listing and in the Figures (see, forexample, FIG. 6 and SEQ ID NO: 1). However, it should be noted, and oneof skill in the art will understand, that different RSV sequences mayhave different numbering systems, for example, if there are additionalamino acid residues added or removed as compared to SEQ ID NO: 1. Assuch, it is to be understood that when specific amino acid residues arereferred to by their number, the description is not limited to onlyamino acids located at precisely that numbered position when countingfrom the beginning of a given amino acid sequence, but rather that theequivalent/corresponding amino acid residue in any and all RSV Fsequences is intended—even if that residue is not at the same precisenumbered position, for example if the RSV sequence is shorter or longerthan SEQ ID NO. 1, or has insertions or deletions as compared to SEQ IDNO. 1. One of skill in the art can readily determine what is thecorresponding/equivalent amino acid position to any of the specificnumbered residues recited herein, for example by aligning a given RSV Fsequence to SEQ ID NO. 1 or to any of the other RSV F amino acidsequences provided herein.

The present invention provides RSV F protein and polypeptide amino acidsequences, and compositions and methods comprising such sequences.However, the invention is not limited to the specific RSV F sequencesdisclosed herein. Rather the present invention contemplates variations,modifications and derivatives of the specific sequences provided herein.

In some embodiments, the RSV F polypeptides, proteins or proteincomplexes of the present invention can be derived from (or can comprise,consist essentially of, or consist of) the amino acid sequences of anysuitable RSV F polypeptide, protein or protein complex sequence known inthe art, including, without limitation: the amino acid sequence of RSVsubtype A (for example in soluble form (SEQ ID NO:1, or amino acidresidues 1-513 thereof) or in a full-length form (SEQ ID NO:2)); theamino acid sequence of RSV subtype B (for example in soluble form (SEQID NO:3, or amino acid residues 1-513 thereof) or in full-length form(SEQ ID NO:4)); the amino acid sequence of RSV variant DS-Cav1 (forexample in soluble form (SEQ ID NO:5, or amino acid residues 1-513thereof) or in full-length form (SEQ ID NO:6)); the amino acid sequenceof RSV variant Cav1 (for example in soluble form (SEQ ID NO:7, or aminoacid residues 1-513 thereof) or in full-length form (SEQ ID NO:8)); orthe amino acid sequence of RSV variant DS (for example in soluble form(SEQ ID NO:9, or amino acid residues 1-513 thereof) or in full-lengthform (SEQ ID NO:10)), or any fragment thereof. In some embodiments, theRSV F proteins and polypeptides of the present invention can be derivedfrom (or can comprise, consist essentially of, or consist of) amino acidsequences that have at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 98%, or 99% sequence identity to any known RSV F sequences or RSV Fectodomain sequences (including but not limited to amino acid residues1-513 of SEQ ID NOs:1-10, or SEQ ID NOs:1-10), or to RSV F sequencesfrom any known RSV groups, subgroups, families, subfamilies, types,subtypes, genera, species, strains, and/or clades, or any fragmentthereof. It should be noted that amino acid residues 1-513 of thevarious RSV F sequences provided herein are core RSV F ectodomainsequences. Amino acid residues 514 onwards in all such sequencescomprise additional domains that may be present in some embodiments butnot in others. In some embodiments variants of such additional domainsmay be present. For example, amino acid residues 514 onwards in allsoluble RSV F sequences provided herein comprise an optional foldontrimerization domain, thrombin cleavage site, 6× His-tag (SEQ ID NO:46), and a strep tag. In some embodiments these additional sequences maybe absent, modified, rearranged or replaced. For example, in someembodiments different trimerization domains may be used, or differentepitope tags may be used. Similarly, amino acid residues 514 onwards inall “full-length” or membrane-bound RSV F sequences provided hereincomprise an optional RSV F protein transmembrane region and cytoplasmictail. In some embodiments these additional sequences may be absent,modified, rearranged or replaced, for example with differenttransmembrane or cytoplasmic domains.

In some embodiments the present invention provides RSV F polypeptides,proteins, and/or protein complexes that comprise one or moreartificially-introduced cross-links, wherein at least one of thefollowing amino acid residues within the RSV F polypeptides, proteins,and/or protein complexes is artificially cross-linked to another aminoacid residue in the RSV F protein: Y33, K77, N88, M97, A147, 5150, 5155,H159, N183, V185, V187, Y198, V220, E222, F223, K226, 5255, Y286, K427and V469. In some such embodiments the cross-link is a di-tyrosinecross-link.

In some embodiments the present invention provides RSV F polypeptides,proteins, and/or protein complexes that comprise one or moreartificially-introduced cross-links, wherein such artificiallyintroduced cross-links connect two of the following amino acid residues:Y33, K77, N88, M97, A147, 5150, 5155, H159, N183, V185, V187, Y198,V220, E222, F223, K226, S255, Y286, K427 and V469. In some suchembodiment the cross-link is a di-tyrosine cross-link.

In some embodiments the present invention provides RSV F polypeptides,proteins, and/or protein complexes in which the amino acid residues inone or more of the following pairs of amino residues are cross-linked toeach other by an artificially introduced cross-link: 147/286, 198/220,198/222, 198/223, 198/226, 33/496, 77/222, 88/255, 97/159, 183/427,185/427, and 187/427. In some such embodiments the cross-link is adi-tyrosine cross-link.

In some embodiments the present invention provides RSV F polypeptides,proteins, and/or protein complexes comprising an artificially introducedcross-link between two of the following regions: the F1 mobileN-terminus (residues 137-216), α2 (residues 148-160), α3 (residues163-173), γ3 (residues 176-182), β4 (residues 186-195), α4 (residues197-211), the F1 mobile C-terminus (residues 461-513), β22 (residues464-471), α9 (residues 474-479), β23 (residues 486-491), and α10(residues 493-514). In some such embodiments the cross-link is adi-tyrosine cross-link.

In some embodiments the present invention provides RSV F polypeptides,proteins, and/or protein complexes comprising an artificially introducedcross-link between two of the following regions: amino acid residuesfrom about position 67 to about position 87, amino acid residues fromabout position 78 to about position 98, amino acid residues from aboutposition 87 to about position 107, amino acid residues from aboutposition 137 to about position 157, amino acid residues from aboutposition 140 to about position 160, amino acid residues from aboutposition 145 to about position 165, amino acid residues from aboutposition 149 to about position 169, amino acid residues from aboutposition 173 to about position 193, amino acid residues from aboutposition 175 to about position 195, from about position 177 to aboutposition 197, amino acid residues from about position 188 to aboutposition 208, amino acid residues from about position 210 to aboutposition 230, amino acid residues from about position 212 to aboutposition 232, amino acid residues from about position 213 to aboutposition 233, amino acid residues from about position 216 to aboutposition 236, amino acid residues from about position 245 to aboutposition 265, amino acid residues from about position 276 to aboutposition 296, amino acid residues from about position 417 to aboutposition 437, and amino acid residues from about position 459 to aboutposition 479. In some such embodiments the cross-link is a di-tyrosinecross-link.

In embodiments where the RSV F polypeptides, proteins, and/or proteincomplexes of the invention comprise one or more di-tyrosine cross-links,di-tyrosine cross-links may be introduced between two endogenoustyrosine residues, between two tyrosine residues originating from“to-tyrosine” mutations, or between a tyrosine residue originating froma “to-tyrosine” mutation and an endogenous tyrosine residue. In someembodiments, more than one di-tyrosine cross-link is introduced into aRSV F protein or polypeptide.

In embodiments where the RSV F polypeptides, proteins, and/or proteincomplexes of the invention comprise one or more di-tyrosine cross-links,non-limiting examples of amino acid positions where a “to-tyrosine”mutation can be introduced include K77, N88, M97, A147, S150, S155,H159, N183, V185, V187, V220, E222, F223, K226, S255, K427 and V469 (seeFIG. 6), or any combination thereof.

In embodiments where the RSV F polypeptides, proteins, and/or proteincomplexes of the invention comprise one or more di-tyrosine cross-links,non-limiting examples of preexisting or endogenous tyrosine residuesthat can be used to form a di-tyrosine cross-link include Y33, Y198 andY286 (see FIG. 6), or any combination thereof.

In embodiments where the RSV F polypeptides, proteins, and/or proteincomplexes of the invention comprise one or more di-tyrosine cross-links,non-limiting examples of residue pairs between which a di-tyrosinecross-link can be introduced include 147/286, 198/220, 198/222, 198/223,198/226, 33/496, 77/222, 88/255, 97/159, 183/427, 185/427, and 187/427,or any combination thereof.

In embodiments where the RSV F polypeptides, proteins, and/or proteincomplexes of the invention comprise one or more di-tyrosine cross-links,non-limiting examples of regions or secondary structures of the RSV Fprotein from which amino acids may be selected for tyrosine substitutionand/or di-tyrosine cross-linking include the F1 mobile N-terminus(residues 137-216), α2 (residues 148-160), α3 (residues 163-173), β3(residues 176-182), β4 (residues 186-195), α4 (residues 197-211), the F1mobile C-terminus (residues 461-513), β22 (residues 464-471), α9(residues 474-479), β23 (residues 486-491), and α10 (residues 493-514).Non-limiting examples of other regions of RSV F protein from which oneor more amino acids may be selected for tyrosine substitution and/orcross-linking include residues from about position 67 to about position87, from about position 78 to about position 98, from about position 87to about position 107, from about position 137 to about position 157,from about position 140 to about position 160, from about position 145to about position 165, from about position 149 to about position 169,from about position 173 to about position 193, from about position 175to about position 195, from about position 177 to about position 197,from about position 188 to about position 208, from about position 210to about position 230, from about position 212 to about position 232,from about position 213 to about position 233, from about position 216to about position 236, from about position 245 to about position 265,from about position 276 to about position 296, from about position 417to about position 437, and from about position 459 to about position479.

In some embodiments, the present invention provides RSV F polypeptides,proteins, and/or protein complexes that are derived from, comprise,consist essentially of, or consist of, the amino acid sequence of SEQ IDNO:11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, or 32, or amino acid residues 1-513 thereof, (each ofwhich are mutants of the RSV F amino acid sequence that comprise one ormore “to tyrosine” mutations to facilitate di-tyrosine cross-linking andto facilitate “locking” of the RSV F protein in its pre-F conformation),or any fragment thereof, such as fragments comprising amino acidresidues 1-513 thereof, and/or fragments comprising the F1 or F2fragments of the RSV F protein, or any other fragments of the RSV Fprotein that may be generated proteolytically and/or that may beassembled into or form part of a functional RSV F protein. In someembodiments, the present invention provides RSV F polypeptides,proteins, and/or protein complexes that are derived from, comprise,consist essentially of, or consist of, an amino acid sequence having atleast about 75%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity toSEQ ID NO: 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, or 32, or amino acid residues 1-513 thereof, orany fragment thereof.

Non-limiting examples of amino acid positions in an RSV F protein orpolypeptide to which di-tyrosine cross-links may be targeted include Y33(pre-existing Tyr residue) and V469Y (to-Tyr substitution), where aF2-F1 intra-protomer bond will form, the positions Y198 (pre-existingTyr residue) and E222Y (to-Tyr substitution), where an F1-F1intra-molecular bond would form, the positions K77Y (to-Tyrsubstitution) and E222Y (to-Tyr substitution), where an F₂-F₁inter-protomer bond would form, the positions N88Y (to-Tyr substitution)and S255Y (to-Tyr substitution), where an F₂-F₁ inter-protomer bondwould form, the positions M97Y (to-Tyr substitution) and H159Y (to-Tyrsubstitution), where an F₂-F₁ inter-protomer bond would form, thepositions V185Y (to-Tyr substitution) and K427Y (to-Tyr substitution),where an F₁-F₁ inter-protomer bond would form, and the positions N183Y(to-Tyr substitution) and K427Y (to-Tyr substitution), where an F₁-F₁inter-protomer bond would form. These positions were initiallyidentified by analysis of the atomic level structure of the RSVprefusion F protein. Further non-limiting examples include positionsA147Y (to-Tyr substitution) and Y286 (pre-existing Tyr), Y198(pre-existing Tyr residue) and V220Y (to-Tyr substitution), Y198(pre-existing Tyr residue) and F223Y (to-Tyr substitution), Y198(pre-existing Tyr residue) and K226Y (to-Tyr substitution), V187Y(to-Tyr substitution) and K427Y (to-Tyr substitution) and N88Y (to-Tyrsubstitution) and S255Y (to-Tyr substitution). In some embodiments, theRSV polypeptides, proteins or protein complexes of the inventioncomprise one of the above listed di-tyrosine cross-links. In someembodiments, the RSV polypeptides, proteins or protein complexes of theinvention comprise two of the above listed di-tyrosine cross-links. Insome embodiments, the RSV polypeptides, proteins or protein complexes ofthe invention comprise three of the above listed di-tyrosinecross-links. In some embodiments, the RSV polypeptides, proteins orprotein complexes of the invention comprise four of the above listeddi-tyrosine cross-links. In some embodiments, the RSV polypeptides,proteins or protein complexes of the invention comprise five or more ofthe above listed di-tyrosine cross-links. In some embodiments, the RSVpolypeptides, proteins or protein complexes of the invention compriseany combination or one or more of the above listed di-tyrosinecross-links.

Non-limiting examples of RSV F proteins designed to have more than onedi-tyrosine cross-link include RSV F proteins with two “to-tyrosine”mutations (E222Y/V469Y), for example, derived from subtype A (SEQ IDNO:29) or DS-Cav1 (SEQ ID NO:31) where the tyrosine substituted atposition 222 is designed to pair with the endogenous tyrosine atposition 198, and the tyrosine substituted at position 469 is designedto pair with the endogenous tyrosine at position 33, thus stabilizingthe RSV F protein by the formation of two di-tyrosine cross-links; andRSV F proteins with two to-tyrosine mutations (K226Y/V469Y), forexample, derived from subtype A (SEQ ID NO:30) or DS-Cav1 (SEQ ID NO:32)where the tyrosine substituted at position 226 is designed to pair withthe endogenous tyrosine at position 198, and the tyrosine substituted atposition 469 is designed to pair with the endogenous tyrosine atposition 33, thus stabilizing the F protein by the formation of twodi-tyrosine cross-links.

As described above, each protomer of the mature RSV F trimer may becleaved into two distinct polypeptide chains termed F1 and F2 whichassociate non-covalently to form a protomer. A bond between a F1polypeptide and a F2 polypeptide within the same protomer is an exampleof an inter-molecular bond and an intra-protomer bond. The inventionprovides exemplary RSV F proteins and polypeptides comprisingcross-links designed to stabilize this interaction, including withoutlimitation, SEQ ID NO:16 (V469Y, where the introduced tyrosine atposition 469 is designed to pair with endogenous tyrosine 33), SEQ IDNO:17 (K77Y/E222Y, designed to form a di-tyrosine pair between theintroduced tyrosines), SEQ ID NO:18 (N88Y/S255Y, designed to form adi-tyrosine pair between the introduced tyrosines), and SEQ ID NO:19(M97Y/H159Y, designed to form a di-tyrosine pair between the introducedtyrosines), as well as RSV F polypeptides, proteins or protein complexesderived from such sequences and including the specific “to tyrosine”mutations present in such sequences. The invention also providesexemplary RSV F proteins and polypeptides comprising cross-linksdesigned to hold two protomers of the trimer together (inter-molecular,inter-protomer bond), including without limitation, SEQ ID NO:20(V185Y/K427Y), SEQ ID NO:21 (V187Y/K427Y) SEQ ID NO:22 (N183Y/K427Y), aswell as RSV F polypeptides, proteins or protein complexes derived fromsuch sequences and including the specific “to tyrosine” mutationspresent in such sequences. In each of these proteins, one introducedtyrosine in one protomer is designed to pair with the other introducedtyrosine on the adjacent protomer. For example, in SEQ ID NO:20(V185Y/K427Y), the tyrosine at position 185 on “protomer A” would form adi-tyrosine bond with the tyrosine at position 427 on “protomer B” (seeFIG. 31A).

In some embodiments, the F1 polypeptide of a RSV F protein iscross-linked with the F2 polypeptide of the same protomer(inter-molecular/intra-protomer bond). In some embodiments, the F1polypeptide is intra-molecularly cross-linked (e.g., both tyrosines ofthe cross-link are located within the same F1 polypeptide). In someembodiments, the F2 polypeptide is intra-molecularly cross-linked (e.g.,both tyrosines of the cross-link are located within the same F1polypeptide). In some embodiments, the F1 polypeptide of the RSVprefusion F protein is cross-linked with the F1 polypeptide of anadjacent protomer (inter-protomer bond). In some embodiments, the F1polypeptide of the RSV prefusion F protein is cross-linked with the F2polypeptide of an adjacent protomer (inter-protomer bond).

The transition from the pre-F to the post-F structures involves verysignificant rearrangement of parts of the RSV protein, in particular theC- and N-termini of F₁, while the rest of the protein movessignificantly less. In order to stabilize the preF conformation by themethods of this invention, parts of the protein that move significantly(e.g. more than 5 Å) can be attached to parts of the protein that moveless significantly (e.g. less than 5 Å), either between two residues ofthe F₁ chain of a single protomer, between two residues of the F₂ chainof single protomer, between one residue of the F₁ chain and one residueof the F₂ chain within the same protomer, or between F₁ and/or F₂residues of two adjacent protomers. Alternatively, parts of the proteinthat move significantly (e.g. more than 5 Å) can be attached to otherparts of the protein that also move significantly (e.g. more than 5 Å),also either between two residues of the F₁ chain, between two residuesof the F₂ chain, between one residue of the F₁ chain and one residue ofthe F₂ chain of within the same protomer, or between F₁ and/or F₂residues of two adjacent protomers. Covalent attachment of moving partsto either moving or non-moving parts prevents the transition from theprefusion structure to either intermediate structures or to thepostfusion structure.

Positions in F₂ that move more than 5 Å in the pre-fusion to post-fusiontransition include the positions 62 through 76, whereas positions 26through 61 and 77 through 97 move less than 5 Å (and positions 98-109have yet to be determined in the pre-fusion structure). Positions in F₁that move more than 5 Å in the pre-F to post-F transition include thepositions 137 through 216 (F₁ mobile N-terminus) and 461 through 513 (F₁mobile C-terminus). The F₁ mobile N-terminus of the preF structurefurther comprises the □2 (positions 148 through 173), □

(positions 1

6 through 1

), and □4 (positions 197 through 211) secondary structures that can eacheither be attached to one another, or to other moving or non-movingparts within the same protomer or between protomers of the F proteintrimer (complex consisting of three protomers). The F₁ mobile C-terminusof the preF structure further comprises the □22 (positions 464 479), □□3(positions 486 t structures that can each either be attached to oneanother, or to other moving or non-moving parts within the same protomeror between protomers of the F protein trimer. (See FIG. 32.)

In some embodiments (including all of those described above, and thoseinvolving RSV F polypeptides, proteins, and/or protein complexes havingany of the specific amino acid sequences recited herein, and thoseinvolving variants or fragments of such RSV F polypeptides, proteins,and/or protein complexes having less than 100% identity to the specificamino acid sequence provided herein), the RSV F polypeptides, proteins,and/or protein complexes of the invention should have one or moredesired properties such as being capable of (1) forming the pre-Fconformation, (2) being “locked” in the pre-F conformation bycross-linking, (3) binding to a pre-F specific antibody, (4) binding toan antibody that binds to site ø, (5) binding to a neutralizingantibody, (6) binding to a broadly neutralizing antibody, (7) binding toan antibody selected from the group consisting of D25, AM22, 5C4, 101F(8) binding to palivizumab (Synagis), (9) binding to and/or activating aB cell receptor, (10) eliciting an antibody response in an animal, (11)eliciting a protective antibody response in an animal, (12) elicitingproduction of neutralizing antibodies in an animal, (13) elicitingproduction of broadly neutralizing antibodies in an animal, (14)eliciting production of antibodies that recognize quaternaryneutralizing epitopes (QNEs) in an animal, and/or (15) eliciting aprotective immune response in an animal.

Unless otherwise stated, all description herein that relates to specificRSV F polypeptides, proteins, and protein complexes, relates equally toall homologs, orthologs, analogs, derivatives, mutant forms, fragments,chimeras, fusion proteins etc. thereof, such as those that have certaindesired properties or features (for example those that are in the pre-Fconformation, or that are capable of forming part of a complex havingthe desired pre-F conformation, or that have desired functionalproperties, including, but not limited to, being capable of binding to,or eliciting the production of, one or more anti-RSV antibodies, such asantibodies that are specific to the RSV pre-F conformation and/or thatbind to the ø site).

Similarly, all description herein that relates to specific polypeptides,proteins, and/or protein complexes polypeptides, proteins, and/orprotein complexes (e.g. those having specific amino acid sequences orthose from a specific RSV type, subtype, or strain) relates equally toother related forms of such polypeptides, proteins, and/or proteincomplexes that may exist in nature (for example in different RSV types,subtypes or strains) or that are related to the specific sequencesprovides herein but have been altered artificially in some way, such asby recombinant means, chemical means, or any other means. Thepolypeptides, proteins, and/or protein complexes described herein canhave, or can be derived from, the nucleotide and/or amino acid sequencesof any suitable RSV polypeptides, proteins, and/or protein complexesknown in the art. In some embodiments, the RSV F polypeptides, proteins,and/or protein complexes of the invention may be, or may be derivedfrom, derivatives and/or analogs of specific RSV F polypeptides,proteins, and/or protein complexes described herein or known in the art,including proteins that are substantially homologous to any suchproteins, or fragments thereof (e.g., in various embodiments, thosehaving at least about 40% or 50% or 60% or 70% or 75% or 80% or 85% or90% or 95% or 98% or 99% identity with an amino acid or nucleic acidsequence of any specific RSV F polypeptides, proteins, and/or proteincomplexes described herein or known in the art, when aligned using anysuitable method known to one of ordinary skill in the art, such as, forexample, using a computer homology program known in the art) or whoseencoding nucleic acid is capable of hybridizing to a coding nucleic acidsequence of a protein of the invention, under high stringency, moderatestringency, or low stringency conditions.

In some embodiments, the invention provides fragments of the specificRSV F polypeptides, proteins, and protein complexes described herein,such as those comprising, consisting essentially of, or consisting of,at least about 10 amino acids, 20 amino acids, 50 amino acids, 100 aminoacids, 200 amino acids, or 500 amino acids.

In some embodiments one or more amino acid residues within a specificRSV F polypeptide, protein, and/or protein complex as described herein,or as known in the art, can be deleted, added, or substituted withanother amino acid. In embodiments where such mutations are introduced,the RSV F polypeptides, proteins, or protein complexes can bemicro-sequenced to determine a partial amino acid sequence. In otherembodiments the nucleic acid molecules encoding the RSV F polypeptides,proteins, and/or protein complexes can be sequenced to identify and/orconfirm the introduction of mutations.

In some embodiments, one or more amino acid residues can be substitutedby another amino acid having a similar polarity and that may acts as afunctional equivalent, resulting in a silent alteration. In someembodiments substitutions for an amino acid within the sequence may beselected from other members of the class to which the amino acid belongse.g. to create a conservative substitution. For example, the nonpolar(hydrophobic) amino acids include alanine, leucine, isoleucine, valine,proline, phenylalanine, tryptophane and methionine. The polar neutralamino acids include glycine, serine, threonine, cysteine, tyrosine,asparagine, and glutamine. The positively charged (basic) amino acidsinclude arginine, lysine and histidine. The negatively charged (acidic)amino acids include aspartic acid and glutamic acid. Such substitutionsare generally understood to be conservative substitutions.

In some embodiments artificial, synthetic, or non-classical amino acidsor chemical amino acid analogs can be used to make the RSV Fpolypeptides, proteins, and/or protein complexes of the invention.Non-classical amino acids include, but are not limited to, the D-isomersof the common amino acids, fluoro-amino acids, and “designer” aminoacids such as β-methyl amino acids, Cγ-methyl amino acids, Nγ-methylamino acids, and amino acid analogs in general. Additional non-limitingexamples of non-classical amino acids include, but are not limited to:α-aminocaprylic acid, Acpa; (S)-2-aminoethyl-L-cysteine/HCl, Aecys;aminophenylacetate, Afa; 6-amino hexanoic acid, Ahx; γ-amino isobutyricacid and α-aminoisobytyric acid, Aiba; alloisoleucine, Aile;L-allylglycine, Alg; 2-amino butyric acid, 4-aminobutyric acid, andα-aminobutyric acid, Aba; p-aminophenylalanine, Aphe; b-alanine, Bal;p-bromophenylalaine, Brphe; cyclohexylalanine, Cha; citrulline, Cit;β-chloroalanine, Clala; cycloleucine, Cle; p-cholorphenylalanine, Clphe;cysteic acid, Cya; 2,4-diaminobutyric acid, Dab; 3-amino propionic acidand 2,3-diaminopropionic acid, Dap; 3,4-dehydroproline, Dhp;3,4-dihydroxylphenylalanine, Dhphe; p-flurophenylalanine, Fphe;D-glucoseaminic acid, Gaa; homoarginine, Hag; δ-hydroxylysine/HCl, Hlys;DL-β-hydroxynorvaline, Hnvl; homoglutamine, Hog; homophenylalanine,Hoph; homoserine, Hos; hydroxyproline, Hpr; p-iodophenylalanine, Iphe;isoserine, Ise; α-methylleucine, Mle;DL-methionine-S-methylsulfoniumchloide, Msmet; 3-(1-naphthyl) alanine,1Nala; 3-(2-naphthyl) alanine, 2Nala; norleucine, Nle; N-methylalanine,Nmala; Norvaline, Nva; O-benzylserine, Obser; O-benzyltyrosine, Obtyr;O-ethyltyrosine, Oetyr; O-methylserine, Omser; O-methylthreonine, Omthr;O-methyltyrosine, Omtyr; Ornithine, Orn; phenylglycine; penicillamine,Pen; pyroglutamic acid, Pga; pipecolic acid, Pip; sarcosine, Sar;t-butylglycine; t-butylalanine; 3,3,3-trifluroalanine, Tfa;6-hydroxydopa, Thphe; L-vinylglycine, Vig;(−)-(2R)-2-amino-3-(2-aminoethylsulfonyl) propanoic aciddihydroxochloride, Aaspa; (2S)-2-amino-9-hydroxy-4,7-dioxanonanoic acid,Ahdna; (2S)-2-amino-6-hydroxy-4-oxahexanoic acid, Ahoha;(−)-(2R)-2-amino-3-(2-hydroxyethylsulfonyl) propanoic acid, Ahsopa;(−)-(2R)-2-amino-3-(2-hydroxyethylsulfanyl) propanoic acid, Ahspa;(2S)-2-amino-12-hydroxy-4,7,10-trioxadodecanoic acid, Ahtda;(2S)-2,9-diamino-4,7-dioxanonanoic acid, Dadna;(2S)-2,12-diamino-4,7,10-trioxadodecanoic acid, Datda;(S)-5,5-difluoronorleucine, Dfnl; (S)-4,4-difluoronorvaline, Dfnv;(3R)-1-1-dioxo-[1,4]thiaziane-3-carboxylic acid, Dtca;(S)-4,4,5,5,6,6,6-heptafluoronorleucine, Hfnl;(S)-5,5,6,6,6-pentafluoronorleucine, Pfnl;(S)-4,4,5,5,5-pentafluoronorvaline, Pfnv; and(3R)-1,4-thiazinane-3-carboxylic acid, Tca. Furthermore, the amino acidcan be D (dextrorotary) or L (levorotary). For a review of classical andnon-classical amino acids, see Sandberg et al., 1998 (Sandberg et al.,1998. New chemical descriptors relevant for the design of biologicallyactive peptides. A multivariate characterization of 87 amino acids. JMed Chem 41(14): pp. 2481-91).

Nucleic Acids

In addition to providing certain RSV F polypeptides, proteins, and/orprotein complexes, as described herein, the present invention alsoprovides nucleic acids encoding such RSV F polypeptides, proteins,and/or protein complexes, and compositions and vectors comprising suchnucleic acids. Such nucleic acids can be obtained or made using anysuitable method known in the art. For example, nucleic acid moleculesencoding RSV F polypeptides, proteins, and/or protein complexes may beobtained from cloned DNA or made by chemical synthesis. In someembodiments the nucleic acids may be obtained by reverse transcribingRNA prepared by any of the methods known to one of ordinary skill in theart, such as random- or poly A-primed reverse transcription. Whateverthe source, a nucleic acid molecule encoding a RSV F polypeptide,protein, and/or protein complex of the present invention can be clonedinto any suitable vector, such as those to be used for propagation ofthe nucleic acid molecule or those to be used for expression of thenucleic acid molecule. The nucleic acid may be cleaved at specific sitesusing various restriction enzymes, if needed. In embodiments requiringexpression, the nucleic acid can be operatively linked to a promotersuitable for directing expression in the desired cell type, such as amammalian cell or an insect cell, and may be incorporated into anysuitable expression vector, such as a mammalian or insect expressionvector.

In some embodiments, the RSV F polypeptides, proteins or proteincomplexes of the present invention can derived from nucleic sequencesthat encode (or that comprise, consist essentially of, or consist ofnucleotide sequences that encode) any suitable RSV F polypeptide,protein or protein complex sequence known in the art, or any fragmentthereof, including, without limitation: a nucleotide sequence thatencodes the wild-type (WT) full length F protein from RSV subtype A (forexample, SEQ ID NO:33), or a nucleotide sequence that encodes thewild-type (WT) full length F protein from RSV subtype B (for example,SEQ ID NO:34), or variants of such sequences that have been codonoptimized for expression in cells of any particular species of interest,or that contain any mutations of interest. For example, in someembodiments, the RSV F polypeptides, proteins or protein complexes ofthe present invention can derived from nucleotide sequences that encodethe F protein of RSV F type A, but that have been codon optimized forexpression in human (e.g. SEQ ID NO:35), hamster (e.g. SEQ ID NO:36),insect (e.g. SEQ ID NO:37), or mouse cells (e.g. SEQ ID NO:38), oroptimized for expression in any other cell type. Similarly, in someembodiments, the RSV F polypeptides, proteins or protein complexes ofthe present invention can derived from nucleotide sequences that encodethe F protein of RSV F type B, but that have been codon optimized forexpression in human (e.g. SEQ ID NO:39), hamster (e.g. SEQ ID NO:40),insect (e.g. SEQ ID NO:41), or mouse cells (e.g. SEQ ID NO:42), oroptimized for expression in any other cell type. Similarly, in someembodiments, the RSV F polypeptides, proteins or protein complexes ofthe present invention can derived from nucleotide sequences that encodethe F protein of RSV F type A or B, and which may or may not have beencodon optimized for expression cells of any given species of interest,and which also comprise one or more other mutations of interest. Forexample, in some embodiments, the RSV F polypeptides, proteins orprotein complexes of the present invention can be derived fromnucleotide sequences that comprise DS-CAV1 (SEQ ID NO:43), DS (SEQ IDNO: 44), and/or CAV1 (SEQ ID NO:45) mutant sequences. Although the threespecific sequences provided in SEQ ID NO:s 43, 44, and 45 comprise theDS, CAV1, and DS-CAV1 mutations in the context of a human codonoptimized full-length RSV type A sequence, such mutations, or indeed anyother mutations of interest (including all of the “to-tyrosine”mutations of the invention), could equally be present in a backbone ofany other suitable RSV type A or type B sequence, including, but notlimited to, those sequences that have been optimized for expression inany species of interest, or that include any mutations of interest, orthat include only certain portions of the RSV type A or B sequences,such as, for example, only nucleotides 1-1539 that encode only the RSV Fectodomain (without the transmembrane and/or cytoplasmic domains). Oneof skill in the art will recognize that there are a variety ofnucleotide sequences that can encode the various RSV F polypeptides andproteins described herein, and all such nucleotide sequences areintended to fall within the scope of the present invention. For example,in some embodiments, the RSV F proteins and polypeptides of the presentinvention can be derived from nucleotide sequences that have at leastabout 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% sequenceidentity to any known nucleotide sequences that encode an RSV F protein,including, but not limited to, any of those illustrated herein(including SEQ ID NOs: 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,and 45), or that have at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 98%, or 99% sequence identity to nucleotides 1-1539 thereof (whichencode the ectodomain sequences), or that have at least about 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity tonucleotide sequences that encode RSV F proteins from any known RSVgroups, subgroups, families, subfamilies, types, subtypes, genera,species, strains, and/or clades, or any fragment thereof.

Furthermore, one or skill in the art can readily visualize, or make,nucleic acid molecules that comprise any one or more of the specific“to-tyrosine” mutations described herein, for example, by locating thenucleotide codon that encodes the specific amino acid residue to bemutated, and mutating the nucleotides at that codon as necessary toresult in a tyrosine-encoding codon.

Cross-Linking

In some embodiments the RSV F polypeptides and/or proteins of theinvention are assembled into protein complexes having a desiredconformational structure, such as the pre-F conformation, and arecross-linked in order to stabilize that conformation. Details ofparticular regions of the RSV F protein that can be cross-linked, aswell as particular RSV mutants designed to facilitate suchcross-linking, are described in other sections of this application. Insome embodiments the cross-links may be used to stabilize the tertiaryand/or quarternary structures of the RSV prefusion F protein. In someembodiments, the cross-linking may be intra- and/or intermolecularcross-linking. In some embodiments, the cross-links that are used aretargeted cross-links. In some embodiments, the cross-links that are usedare stable under physiological conditions. In some embodiments, thecross-links that are used do not lead to aggregate formation of the RSVprefusion F protein, for example during expression and/or during storage(such as storage of compositions comprising high concentrations of theRSV prefusion F protein). In some embodiments the introduction of suchcross-links may enhance the effectiveness of the RSV polypeptides,proteins and proteins of the invention as immunogens, such as vaccineimmunogens. In some embodiments the introduction of such cross-links maystabilize epitopes (such as the φ epitope) within the RSV F protein suchthat the epitopes can be recognized by particular antibodies, elicitproduction of antibodies, and/or activate B cell receptors upon antibodybinding.

In some embodiments targeted cross-linking can be used. A targetedcross-link is one that can be made to form at a particular position orpositions within the RSV F protein or protein complex. Severalstrategies may be used to target cross-links to specific locations in anRSV F protein or polypeptide, such as the specific locations describedherein. The present invention provides residue pairs within the RSV Fprotein that, when cross-linked, can or may stabilize a RSV Fpolypeptide, protein, or protein complex in its pre-F conformation,and/or in a conformation that is capable of binding to, or eliciting theproduction of, neutralizing antibodies, and/or that is capable ofgenerating a neutralizing antibody response in an animal. A targetedcross-link may be introduced at one or more of the locations orpositions specified herein by exploiting the physical and/or chemicalproperties of certain amino acid side chains, for example by making useof enzymatic reactions that recognize specific amino acid sequences orthree-dimensional structures, or by incorporating non-natural aminoacids that have the ability to form cross-links in a folded protein orprotein complex.

Cross-links or modifications may be targeted to specific sites in thestructure of the RSV F protein or polypeptide in order to achieve thedesired outcome, e.g. stabilization or the pre-F conformation. Thepresent invention contemplates the targeted introduction of one or morecross-links and/or other stabilizing modifications at any suitableposition(s) in a RSV F protein or polypeptide, preferably where thecross-link or modification stabilizes the RSV F protein or polypeptidein a pre-fusion conformation, or provides enhanced stabilization of thepre-fusion conformation. The invention contemplates that any RSV Fprotein amino acid residue, residue pair, secondary structure or otherregion described herein for di-tyrosine cross-linking may also be usedin the formation of other targeted cross-links or bonds or othermodifications, including but not limited to amino acid positions Y33,K77, N88, M97, A147, S150, S155, H159, N183, V185, V187, Y198, V220,E222, F223, K226, S255, Y286, K427 and V469, or any combination thereof;residue pairs 147/286, 198/220, 198/222, 198/223, 198/226, 33/496,77/222, 88/255, 97/159, 183/427, 185/427, and 187/427, or anycombination thereof; regions or secondary structures including the F1mobile N-terminus (residues 137-216), α2 (residues 148-160), α3(residues 163-173), β3 (residues 176-182), β4 (residues 186-195), α4(residues 197-211), the F1 mobile C-terminus (residues 461-513), β22(residues 464-471), α9 (residues 474-479), β23 (residues 486-491), andα10 (493-514); and other regions of RSV F protein including residuesfrom about position 67 to about position 87, from about position 78 toabout position 98, from about position 87 to about position 107, fromabout position 137 to about position 157, from about position 140 toabout position 160, from about position 145 to about position 165, fromabout position 149 to about position 169, from about position 173 toabout position 193, from about position 175 to about position 195, fromabout position 177 to about position 197, from about position 188 toabout position 208, from about position 210 to about position 230, fromabout position 212 to about position 232, from about position 213 toabout position 233, from about position 216 to about position 236, fromabout position 245 to about position 265, from about position 276 toabout position 296, from about position 417 to about position 437, andfrom about position 459 to about position 479.

A wide variety of methods of cross-linking proteins intra- andinter-molecularly are known in the art, including those havingcross-links with varying lengths of spacer arms, and those with andwithout fluorescent and functional groups for purification. Such methodsinclude, but are not limited to, the use of heterobifunctionalcross-linkers (e.g. succinimidyl acetylthioacetate (SATA),trans-4-(maleimidylmethyl) cyclohexane-1-carboxylate (SMCC), andsuccinimidyl 3-(2-pyridyldithio)propionate (SPDP)), homobifunctionalcross-linkers (e.g. succinimidyl 3-(2-pyridyldithio)propionate),photoreactive cross-linkers (e.g. 4-azido-2,3,5,6-tetrafluorobenzoicacid, STP ester, sodium salt (ATFB, STP ester),4-azido-2,3,5,6-tetrafluorobenzoic acid, succinimidyl ester (ATFB, SE),4-azido-2,3,5,6-tetrafluorobenzyl amine, hydrochloride,benzophenone-4-isothiocyanate, benzophenone-4-maleimide,4-benzoylbenzoic acid, succinimidyl ester,N-((2-pyridyldithio)ethyl)-4-azidosalicylamide (PEAS; AET), thiolreactive cross-linkers (e.g. maleimides and iodoacetamides), aminereactive cross-linkers (e.g. glutaraldyde, bis(imido esters),bis(succinimidyl esters), diisocyanates and diacid chlorides). Becausethiol groups are highly reactive and relatively rare in most proteins bycomparison to amine groups, thiol-reactive cross-linking may be used insome embodiments. In cases where thiol groups are missing or not presentat appropriate sites in the structures of RSV prefusion F protein, theycan be introduced using one of several thiolation methods. For example,Succinimidyl trans-4-(maleimidylmethyl)cyclohexane-1-carboxylate can beused to introduce thiol-reactive groups at amine sites.

Several oxidative cross-links are known, such as disulfide bonds (whichform spontaneously and are pH and redox sensitive), and di-tyrosinebonds (which are highly stable, and irreversible under physiologicalconditions).

In some embodiments the cross-links stabilize the tertiary structure ofa RSV pre-fusion F protein. In some embodiments the cross-linksstabilize the quaternary structure of a RSV pre-fusion F protein. Insome embodiments the cross-links stabilize both the tertiary andquaternary structure of a RSV pre-fusion F protein.

In some embodiments a RSV F protein or polypeptide of the invention hascross-links that are thermostable. In some embodiments a RSV F proteinor polypeptide of the invention has cross-links that are not toxic. Insome embodiments a RSV F protein or polypeptide of the invention hascross-links that are targeted cross-links, or non-targeted cross-links,or reversible cross-links, or irreversible cross-links, or cross-linksformed by use of homo-bifunctional cross-linking agents, or cross-linksformed by use of hetero-bifunctional cross-linking agents, orcross-links formed by use of reagents that react with amine groups, orcross-links formed by use of reagents that react with thiol groups, orcross-links formed by use of reagents that are photoreactive, orcross-links formed between amino acid residues, or cross-links formedbetween mutated amino acid residues incorporated into the structure ofthe proteins or protein complexes, or oxidative cross-links, ordi-tyrosine bonds, or glutaraldehyde cross-links, or any combinationthereof. In some embodiments the RSV F protein or polypeptide of theinvention does not have glutaraldehyde cross-links.

In some embodiments the RSV F protein or polypeptide of the inventiondoes not have any artificially-introduced disulfide bonds, or if it doeshave such disulfide bonds, also has additional artificially-introducedcross-links. In some embodiments the RSV F protein or polypeptide of theinvention does not have any artificially introduced disulfide bonds, butmay have naturally occurring disulfide bonds. Disulfide bonds can beintroduced artificially when cysteine side-chains are engineered bypoint mutation. Disulfide bonds are, however, known to be pH sensitiveand to be dissolved under certain redox conditions, and the preventativeand/or therapeutic utility of proteins and/or protein complexesengineered with disulfide cross-links, for example to be used asimmunogens in vivo, may therefore be compromised. Furthermore, undesireddisulfide bonds often form between proteins with free sulfhydryl groupsthat mediate aggregate formation (see, for example, Harris R J et al.2004, Commercial manufacturing scale formulation and analyticalcharacterization of therapeutic recombinant antibodies. Drug Dev Res 61(3): 137-154; Costantino & Pikal (Eds.), 2004. Lyophilization ofBiopharmaceuticals, editors Costantino & Pekal. Lyophilization ofBiopharmaceuticals. Series: Biotechnology: Pharmaceutical Aspects II,see pages 453-454; Tracy et al., 2002, U.S. Pat. No. 6,465,425), whichhas also been reported as a problem with HIV gp120 and gp41 (Jeffs etal. 2004. Expression and characterization of recombinant oligomericenvelope glycoproteins derived from primary isolates of HIV-1. Vaccine22:1032-1046; Schulke et al., 2002. Oligomeric and conformationalproperties of a proteolytically mature, disulfide-stabilized humanimmunodeficiency virus type 1 gp140 envelope glycoprotein. J Virol76:7760-7776). Thus, in many embodiments it is preferred that disulfidebonding is not used, or is not used as the sole method of cross-linking.

If the structure and/or immunogenicity of the RSV prefusion F protein iscompromised or altered by a cross-link, maintaining its overallstructure and function can be achieved by controlling the availabilityof amino acid side-chains for the cross-linking reaction or byintroducing additional cross-links or other stabilizing modifications.For example, in the case of DT cross-linking, tyrosyl side-chains thatare available for reaction, but that lead to the distortion of thestructure of the complex, and that compromise theimmunogenicity/antigenicity of the RSV F protein, can be removed bymutating such residues to another amino acid such as, for example,phenylalanine. Furthermore, point mutations may be introduced atpositions where the amino acid side-chains will react with cross-linkingagents or each other, such that the formation of the bond(s) causes themost beneficial outcome. These positions may also be identified asdescribed herein.

When at a selected residue a reactive side-chain is not already present,a point mutation may be introduced, for example using molecularbiological methods to introduce such a point mutation into the cDNA of anucleic acid directing its expression, such that a reactive side-chainis present and available for the reaction.

Cross-links that may be used include, but are not limited to, reversiblecross-links resulting from the use of homo- and hetero-bifunctionalcross-linking agents that react with amine and/or thiol groups,photoreactive cross-link reagents, any cross-links that may form betweennon-classical amino acids incorporated into the structure of a proteinor protein complex, any oxidative cross-links, such as, but not limitedto, di-tyrosine cross-links/bonds, heterobifunctional cross-linkers(e.g. succinimidyl acetylthioacetate (SATA), trans-4-(maleimidylmethyl)cyclohexane-1-carboxylate (SMCC), and succinimidyl3-(2-pyridyldithio)propionate (SPDP)), homobifunctional cross-linkers(e.g. succinimidyl 3-(2-pyridyldithio)propionate), photoreactivecross-linkers (e.g. 4-azido-2,3,5,6-tetrafluorobenzoic acid, STP ester,sodium salt (ATFB, STP ester), 4-azido-2,3,5,6-tetrafluorobenzoic acid,succinimidyl ester (ATFB, SE), 4-azido-2,3,5,6-tetrafluorobenzyl amine,hydrochloride, benzophenone-4-isothiocyanate, benzophenone-4-maleimide,4-benzoylbenzoic acid, succinimidyl ester,N-((2-pyridyldithio)ethyl)-4-azidosalicylamide (PEAS; AET), thiolreactive cross-linkers (e.g. maleimides and iodoacetamides), aminereactive cross-linkers (e.g. glutaraldyde, bis(imido esters),bis(succinimidyl esters), diisocyanates and diacid chlorides).

The present invention also contemplates the introduction of targetednon-covalent tyrosine-stacking interactions as “cross-links” tostabilize protein-protein interactions and/or desired protein or peptideconformations, such as the pre-fusion conformation of RSV F protein. Thecross-link comprises a targeted pi stacking interaction including butnot limited to a T-shaped, sandwich, or parallel displaced pi stackinginteraction between the aromatic side chains of an introduced/engineeredtyrosine and an endogenous tyrosine, phenylalanine, histidine, ortryptophan within the protein or protein complex, or between thearomatic side chain of an introduced/engineered tyrosine and a secondintroduced/engineered tyrosine within the protein or protein complex.

Irreversible cross-links, as used in the context of this application,include those that are not significantly dissolved under physiologicallyrelevant conditions. It is preferred that the type of cross-links usedshould not lead to aggregate formation during expression or when the RSVF polypeptides, proteins and/or protein complexes of the invention arestored at high concentrations. Disulfide bonds are not irreversiblecross-links. Rather they are reversible cross-links and may dissolveunder physiologically relevant conditions and/or lead to aggregateformation during protein expression and/or production or when stored inhigh concentrations.

In some embodiments cross-links may be targeted to the specific regionsof RSV F polypeptides, proteins and/or protein complexes describedherein in order to achieve the desired conformational stabilizationand/or the desired immunogenic properties (e.g. the ability to maintainthe pre-F conformation and/or to bind to broadly neutralizingantibodies). Alternatively, proteins with the cross-links at thelocations specified herein may be isolated from a mixture ofcross-linked and un-cross-linked proteins with and without desiredmodifications, for example based on chemical, physical, and/orfunctional characteristics. Such characteristics may include, forexample, trimerization, the presence of the pre-F conformation, and/orany desired antigenic, immunogenic, or biochemical characteristics.

Alternatively, in some embodiments, cross-links may not be targeted, andproteins with the desired cross-links or properties may be isolated froma mixture of modified and unmodified proteins made using a non-targetedcross-linking system.

In embodiments where RSV F polypeptides, proteins or protein complexeswith the desired cross-links are to be isolated from a mixture ofcross-linked and un-cross-linked proteins, such isolation or separationmay be performed on the basis of one or more characteristics including,but not limited to, molecular weight, molecular volume, chromatographicproperties, mobility in electrophoresis, antigenic and biochemicalcharacteristics, fluorescence characteristics, solubility, binding toantibodies, structural characteristics, immunological characteristics,or any other suitable characteristics.

In addition to the specific cross-linking positions described herein,additional positions within RSV F polypeptides, proteins or proteincomplexes can be identified at which further cross-links can be made,for example where a reactive side-chain would be able to form a bondwith a reactive side-chain elsewhere on the RSV F protein/complex. Insome embodiments, such additional positions can be selected, forexample, to maintain or improve the immunogenicity/antigenicity of theprotein, polypeptide or protein complex. In some embodiments, suchadditional positions to be cross-linked can be selected in pairs.

Di-Tyrosine (DT) Cross-Linking

In some embodiments the present invention provides RSV F polypeptides,proteins and/or protein complexes that comprise di-tyrosine (DT)cross-links, and methods of making such DT-cross-linked RSV Fpolypeptides, proteins and/or protein complexes.

Di-tyrosine cross-linking introduces one or more covalent carbon-carbonbonds into proteins or protein complexes. This provides a method forstabilizing proteins, protein complexes, and conformations, byintroduction of intra- and/or inter-polypeptide di-tyrosine bonds whilemaintaining their structural and functional integrity (See Marshall etal., U.S. Pat. Nos. 7,037,894 & 7,445,912, the contents of which arehereby incorporated by reference). The minimally altering, andzero-length DT cross-link is not hydrolyzed under physiologicalconditions, and has been demonstrated to maintain proteins' structuralintegrity by liquid chromatography/mass spectrometry (LC/MS).Di-tyrosine cross-links are known to be safe, as they form naturally invivo, both in the context of proteins evolved to utililze their specificcharacteristics (e.g. Elvin C M et al. 2005, Nature 437:999-1002;Tenovuo J & Paunio K 1979, Arch Oral Biol.; 24(8):591-4), and as aconsequence of non-specific protein oxidation (Giulivi et al. 2003,Amino Acids 25(3-4):227-32), and as they are present in large quantitiesin some of our most common foods: DT bonds form the structure of wheatgluten—the quarternary protein structure comprising the gluteninsubunits—e.g. in bread dough during mixing and baking (Tilley et al.2001, Agric. Food Chem 49, 2627). Di-tyrosine bonds do not formspontaneously in vitro. Rather, the enzymatic cross-link reaction iscarried out under optimized conditions to preserve protein structure andfunction. Therefore, non-specific bonding/aggregation does not occur(unlike with disulfide bonding), and therefore large-scale manufacturingof a DT stabilized immunogen may be economically more feasible.

Tyrosyl side-chains are present in many redox enzymes, and catalysis ofthe enzyme-specific reactions often involves tyrosyl radicals that arelong-lived and have comparatively low reactivity. Under optimizedconditions radical formation is specific to tyrosyl side-chains. Inclose proximity, tyrosyl side chains undergo radical coupling and form acovalent, carbon-carbon bond. Tyrosyl radicals that do not react revertto non-radicalized tyrosyl side-chains (Malencik & Anderson, 2003.Di-tyrosine as a product of oxidative stress and fluorescent probe.Amino Acids 25: 233-247). Therefore, tyrosyl side-chains must besituated in close proximity to form DT bonds, either within a singlefolded polypeptide chain, or on closely interacting protein domainswithin a complex. Because a Cα-Cα separation of approximately 5-8 Å is aprerequisite to bond formation (Brown et al., 1998. Determiningprotein-protein interactions by oxidative cross-linking of aglycine-glycine-histidine fusion protein. Biochemistry 37, 4397-4406;Marshall et al. 2006, U.S. Pat. No. 7,037,894), and because no atom isadded in the formation of these bonds, the resulting “staple” is “zerolength” and non-disruptive to the protein structure.

Tyrosines residues to be cross-linked may be naturally present in theprimary structure of the protein to be cross-linked or may be added bycontrolled point mutation. To form DT bonds, proteins with tyrosyl sidechains can be subjected to reaction conditions that lead to theformation of DT bonds. Such conditions are, or become, oxidativereaction conditions, as the DT bond formation reaction is an oxidativecross-linking reaction. In some embodiments the DT cross-linkingreaction conditions yield proteins that are otherwise not, or notdetectably, modified. Such conditions may be obtained by use of enzymesthat catalyze the formation of H₂O₂, such as peroxidases. DT bondformation may be monitored by spectrophotometry with an excitationwavelength of around 320 nm, and fluorescence measured at a wavelengthof around 400 nm (see, for example, FIG. 34), while loss of tyrosylfluorescence is monitored also monitored by standard procedures. Whenloss of tyrosyl florescence is no longer stoichiometric with DT bondformation, the reaction may be stopped by any methods known to oneskilled in the art, such as, for example, by the addition of a reducingagent and subsequent cooling (on ice) or freezing of the sample. Furtherdetails of how to peform DT cross-linking are known in the art and aredescribed in, for example, Marshall et al. 2006, U.S. Pat. No.7,037,894, the contents of which are hereby incorporated by reference.

The major advantages of di-tyrosine cross-linking in protein engineeringinclude (i) the ability to target specific residues for cross-linking(based on the primary, secondary, tertiary, and/or quaternary structuresof proteins and complexes), (ii) minimal structural modification, (iii)specificity of the reaction (tyrosine is the only amino acid known toform cross-links under specific cross-linking conditions); (iv)stability of the linkage, (v) zero length of the cross-link (no atom isadded), and (vi) the scalability of the cross-linking chemistry.

In some embodiments, targeted DT cross-links may be introduced at one ormore of the specific locations in the RSV F protein that are recitedherein. In other embodiments, additional positions within RSV Fpolypeptides, proteins or protein complexes can be identified at whichDT cross-links can be made. In some embodiments, di-tyrosine bonds orcross-links are targeted to specific residue pairs within the structureof a RSV F protein or polypeptide where DT bonds will, or are expectedto, form due to, for example, their close proximity. In some embodimentstyrosyl side chains are already present at amino acid residues to becross-linked. In some cases naturally occurring tyrosine residues mayconstitute either one or both of the paired tyrosine residues necessaryfor di-tyrosine bond formation. However, in other cases the RSV Fpolypeptides, proteins and/or protein complexes of the invention aremutated or engineered to add one or more tyrosine residues, or tosubstitute one or more non-tyrosine residues for tyrosine residues. Suchmutations are referred to herein as “to-tyrosine” mutations, and can beintroduced at locations where it is desirable to form di-tyrosinecross-links/bonds. In some embodiments, the present invention providesmutant RSV F polypeptides, proteins, and/or protein complexes in whichtyrosyl side chains are introduced at desired cross-linking positions byintroducing point mutations to tyrosine in a nucleic acid sequenceencoding the RSV F polypeptide, protein, or protein complex.Alternatively, in some embodiments RSV proteins, polypeptides or proteincomplexes, or portions thereof, may be synthesized to include tyrosineresidues or amino acids having tyrosyl side chains at desiredcross-linking positions. Conversely, in some embodiments the presentinvention provides mutant RSV F polypeptides, proteins, and/or proteincomplexes in which tyrosyl side chains are removed at undesirablecross-linking positions by introducing point mutations from tyrosine ina nucleic acid sequence encoding the RSV F polypeptide, protein, orprotein complex, or RSV F polypeptides, proteins, or protein complexesmay be synthesized to exclude tyrosine residues or amino acids havingtyrosyl side chains at positions where cross-linking is not desired. Forexample, at least one of the tyrosyl side chains can be replaced withanother side chain, such as a phenylalanine side chain (see, forexample, Marshall C P et al., U.S. patent application Ser. No.09/837,235, the contents of which are hereby incorporated by reference).Accordingly, the RSV F polypeptides, proteins and protein complexes ofthe invention may comprise point mutations “to tyrosine” or “fromtyrosine.” Such mutations can be made by altering the nucleic acidsequences that encode the RSV F polypeptides, proteins and/or proteincomplexes of the invention using any suitable mutagenesis methods knownin the art. Alternatively, mutant RSV F polypeptides, proteins and/orprotein complexes may be synthesized, purified, and/or produced by anyother suitable methods known in the art.

In some embodiments, the present invention contemplates the targetedintroduction of one or more di-tyrosine cross-link at any suitableposition(s) in a RSV F polypeptide, protein or protein complex where thecross-link will or may stabilize the RSV F polypeptide, protein orprotein complex in its pre-fusion conformation. Such stabilization maybe achieved, for example, by introducing cross-links that stabilizeinteractions between or within RSV F protein F1 and F2 polypeptidesand/or by introducing cross-links that stabilize the interactionsbetween or within RSV F protein protomers. In some embodiments, the F1polypeptide of a RSV F protein is cross-linked with the F2 polypeptideof the same protomer (inter-molecular/intra-protomer bond). In someembodiments, the F1 polypeptide is intra-molecularly cross-linked (e.g.,both tyrosines of the cross-link are located within the same F1polypeptide). In some embodiments, the F2 polypeptide isintra-molecularly cross-linked (e.g., both tyrosines of the cross-linkare located within the same F1 polypeptide). In some embodiments, the F1polypeptide of the RSV prefusion F protein is cross-linked with the F1polypeptide of an adjacent protomer (inter-protomer bond). In someembodiments, the F1 polypeptide of the RSV prefusion F protein iscross-linked with the F2 polypeptide of an adjacent protomer(inter-protomer bond).

Making and Analyzing RSV F Polypeptides, Proteins, and Protein Complexes

In some embodiments the present invention provides methods for makingthe RSV F polypeptides, proteins, and protein complexes of theinvention. The RSV F polypeptides, proteins, and protein complexes ofthe invention can be made by any suitable means known in the art. Insome embodiments the RSV F polypeptides, proteins, and/or proteincomplexes of the invention can be made by recombinant means. In someembodiments, the RSV F polypeptides, proteins, and/or protein complexesof the invention, or any portion thereof, can be made by chemicalsynthesis means. For example, a peptide corresponding to a portion of aprotein or protein complex as described herein can be synthesized by useof a peptide synthesizer.

Recombinant Production Methods

In embodiments where the RSV F polypeptides, proteins and proteincomplexes of the invention are made by recombinant means, nucleic acidsencoding the RSV F polypeptides, proteins and protein complexes of theinvention can be expressed in any suitable cell type, including, but notlimited to mammalian cells and insect cells (such as SF9 or Hi5 cells,using a baculovirus expression system). Methods for expressingpolypeptides and proteins from nucleic acid molecules are routine andwell known in the art, and any suitable methods, vectors, systems, andcell types known in the art can be used. For example, typically nucleicacid sequences encoding the RSV F polypeptides, proteins and/or proteincomplexes of the invention will be placed into a suitable expressionconstruct containing a suitable promoter, which will then be deliveredto cells for expression.

Chimeric/Fusion Proteins & Oligomerization Domains

In some embodiments it may be desirable to add chimeric domains to theRSV F polypeptides, proteins and/or protein complexes described herein,to produce chimeric proteins/fusion proteins, for example to facilitatethe analysis and/or isolation and/or purification of the RSV Fpolypeptides, proteins and/or protein complexes described herein. Insome embodiments, the RSV F polypeptides, proteins and protein complexesof the invention may comprise leader sequences, precursor polypeptidesequences, secretion signals, localization signals, epitope tags, andthe like. Epitope tags that can be used include, but are not limited to,FLAG tags, glutathione S-transferase (GST) tags, green fluorescentprotein (GFP) tags, hemagglutinin A (HA) tags, histidine (His) tags,luciferase tags, maltose-binding protein (MBP) tags, c-Myc tags, proteinA tags, protein G tags, streptavidin (strep) tags, and the like.

In some embodiments it may be desirable to add oligomerization domainsto facilitate the assembly of RSV F polypeptides, proteins and/orprotein complexes as described herein, and/or to facilitatestabilization of the pre-F conformation, and/or to stabilize otherstructural features of the RSV F polypeptides, proteins and/or proteincomplexes. In some embodiments the oligomerization domains aretrimerization motifs, including, but not limited to, the T4 foldonmotif. There are a wide variety of trimerization domains in naturalproteins that can be used for these purposes including, but not limitedto, those described in Habazettl et al., 2009 (Habazettl et al., 2009.NMR Structure of a Monomeric Intermediate on the EvolutionarilyOptimized Assembly Pathway of a Small Trimerization Domain. J. Mol.Biol. pp. null), Kammerer et al., 2005. (Kammerer et al., 2005. Aconserved trimerization motif controls the topology of short coiledcoils. Proc Natl Acad Sci USA 102 (39): 13891-13896), Innamorati et al.,2006. (Innamorati et al., 2006. An intracellular role for theC1q-globular domain. Cell signal 18(6): 761-770), and Schelling et al.,2007 (Schelling et al., 2007. The reovirus σ-1 aspartic acid sandwich: Atrimerization motif poised for conformational change. Biol Chem 282(15):11582-11589). Stabilizing trimeric protein complexes can also beaccomplished using the GCN4 and T4 fibrinitin motifs (Pancera et al.,2005. Soluble Mimetics of Human Immunodeficiency Virus Type 1 ViralSpikes Produced by Replacement of the Native Trimerization Domain with aHeterologous Trimerization Motif: Characterization and Ligand BindingAnalysis. J Virol 79(15): 9954-9969; Guthe et al., 2004. Very fastfolding and association of a trimerization domain from bacteriophage T4fibritin. J. Mol. Biol. v337 pp. 905-15; Papanikolopoulou et al., 2008.Creation of hybrid nanorods from sequences of natural trimeric fibrousproteins using the fibritin trimerization motif. Methods Mol Biol474:15-33). Heterologous oligomerization motifs may be introduced by anyrecombinant methods known to one of ordinary skill in the art in orderto stabilize the protein-protein interactions of the proteins of thepresent invention.

Chimeric RSV F polypeptides, proteins and/or protein complexes can bemade by any method known to one of ordinary skill in the art, and maycomprise, for example, one or several RSV F polypeptides, proteinsand/or protein complexes of the invention, and/or any fragment,derivative, or analog thereof (for example, consisting of at least adomain of a polypeptide, protein, or protein complex of the invention,or at least 6, and preferably at least 10 amino acids of thereof) joinedat its amino- or carboxy-terminus via a peptide bond to an amino acidsequence of another protein or other protein domain or motif. In someembodiments such chimeric proteins can be produced by any method knownto one of ordinary skill in the art, including, but not limited to,recombinant expression of a nucleic acid encoding a chimeric protein(e.g. comprising a first coding sequence joined in-frame to a secondcoding sequence); ligating the appropriate nucleic acid sequencesencoding the desired amino acid sequences to each other in the propercoding frame, and expressing the chimeric product.

Post Translational Modifications

In some embodiments, the RSV F polypeptides, proteins and proteincomplexes described herein may be altered by adding or removingpost-translational modifications, by adding or removing chemicalmodifications or appendices, and/or by introducing any othermodifications known to those of ordinary skill in the art. Includedwithin the scope of the invention are RSV F polypeptides, proteins andprotein complexes that are modified during or after translation orsynthesis, for example, by glycosylation (or deglycosylation),acetylation (or deacetylation), phosphorylation (or dephosphorylation),amidation (or deamidization), pegylation, derivatization by knownprotecting/blocking groups, proteolytic cleavage, or buy any other meansknown in the art. For example, in some embodiments the RSV Fpolypeptides, proteins and/or protein complexes may be subjected tochemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8protease, NaBH4, acetylation, formylation, oxidation, reduction,metabolic synthesis in the presence of tunicamycin, etc. In someembodiments such posttranslational modifications can be used to renderthe RSV F polypeptides, proteins, and/or protein complexes of thepresent invention more immunogenic, more stable, and/or more capable ofbinding to, or eliciting the production of, neutralizing and broadlyneutralizing antibodies.

Obtaining RSV F in its Pre-F Conformation

In some embodiments the RSV F polypeptides and/or proteins of theinvention are assembled into protein complexes having a desiredconformational structure, such as the pre-F conformation, and arecross-linked in order to stabilize that conformation. As describedelsewhere in the present application, the pre-F conformation of the RSVF protein comprises a trimer formed from three protomers. In someembodiments, prior to and/or during the enzymatic cross-linkingreaction, the RSV F protein may be obtained in (and/or maintained in)the pre-F conformation, for example while cross-linking is performed. Insome embodiments the RSV F protein may be produced and/or isolated insuch a way that most, or substantially all, of the RSV F molecules arepresent in the pre-F conformation. In some embodiments RSV F moleculesin the pre-F conformation may be separated from a mixed population ofRSV F protein molecules comprising some that are in the pre-Fconformation and some that are in other conformations. In someembodiments, the RSV F protein is expressed in cells (for example as itsmembrane bound or soluble form) and spontaneously assembles into itsnormal pre-F conformation. In some embodiments no additionalstabilization may be necessary to retain the RSV F protein in its pre-Fform. In some embodiments the expressed and assembled/folded RSV Fprotein may be kept under particular conditions, or in particularcompositions, that favor formation and/or maintenance of the pre-Fconformation. For example, in some embodiments the RSV prefusion Fprotein may be maintained in the absence of cells—contact with whichmight otherwise trigger a switch to the post-F conformation. The RSVprefusion F protein may be obtained and/or isolated and/or maintained inthe pre-F conformation using any suitable method known in the art,including, but not limited to, standard protein purification methods,such as ion exchange chromatography, size exclusion chromatography,and/or affinity chromatography methods. In some embodiments the RSVprefusion F protein may be expressed in the presence of, co-expressedwith, or contacted with, molecules that bind to the RSV F protein andstabilize it in its pre-F conformation, including, but not limited to,antibodies, small molecules, peptides, and/or peptidomimetics.Non-limiting examples of antibodies that bind to the pre-fusion RSV Fprotein include the 5C4, AM22, and D25 antibodies (see McLellan et al.(2013) Science 342:592-598, which is hereby incorporated by reference inits entirety). In some embodiments, the RSV F protein may be obtained,isolated, or maintained in its pre-F conformation by controlling theionic strength of the media/buffer in which the protein is present (suchas by using high or low ionic strength media). In some embodiments theRSV F protein may be obtained, isolated, or maintained at one or moretemperatures that favor preservation of the pre-F conformation. In someembodiments the RSV F protein may be obtained, isolated, or maintainedover a period of time that diminishes the degree to which the pre-Fconformation lost.

In some embodiments analysis may be performed to confirm that thedesired conformation, such as the pre-F conformation, has been formedand/or maintained in the RSV F protein. Such analysis may be performedprior to cross-linking, during the cross-linking process, after thecross-linking process, or at any combination of such stages. Suchanalysis may comprise any suitable methods known in the art forassessing the 3-dimensional structure of a protein or protein complex,including functional analysis, crystallographic analysis, and the like.In some embodiments such analysis may include assessing binding of theRSV protein to certain antibodies, such as those that are specific tothe pre-F conformation and/or those that are known to bind to the øsite, as described elsewhere herein, including, but not limited to the5C4, AM22, and D25 antibodies.

Protein Purification

In some embodiments the methods for making RSV F polypeptides, proteins,and protein complexes of the invention may comprise purifying the RSV Fpolypeptides, proteins, or protein complexes before, during, or after,one or more steps in the manufacturing process. For example, in someembodiments the RSV F polypeptides, proteins, and/or protein complexesof the invention may be purified after completion of all of themanufacturing steps. In some embodiments the RSV F polypeptides,proteins, and/or protein complexes of the invention may be purifiedbefore commencing the cross-linking process or after one or more of theintermediate method steps in the process, for example, after expressionof an RSV F polypeptide or protein, after assembly of a protein complex,after obtaining the RSV F protein in its pre-F conformation, or duringor after performing a cross-linking reaction. The RSV F polypeptides,proteins, and/or protein complexes of the invention may be isolated orpurified using any suitable method known in the art. Such methodsinclude, but are not limited to, chromatography (e.g. ion exchange,affinity, and/or sizing column chromatography), ammonium sulfateprecipitation, centrifugation, differential solubility, or by any othertechnique for the purification of proteins known to one of ordinaryskill in the art. In specific embodiments it may be necessary toseparate the desirable influenza RSV F polypeptides, proteins, and/orprotein complexes of the invention from those that were not sufficientlycross-linked, or those in which the pre-F conformation was notsufficiently stabilized. This can be done using any suitable systemknown in the art. For example, RSV proteins in the pre-F conformationcan be separated from those that are not in the pre-F conformation usingantibody-based separation methods using pre-F or post-F specificantibodies. The RSV F polypeptides, proteins, and/or protein complexesof the invention may be purified from any source used to produce them.For example, the RSV F polypeptides, proteins, and/or protein complexesof the invention may be purified from sources including insect,prokaryotic, eukaryotic, mono-cellular, multi-cellular, animal, plant,fungus, vertebrate, mammalian, human, porcine, bovine, feline, equine,canine, avian, or tissue culture cells, or any other source. The degreeof purity may vary, but in various embodiments, the purified RSV Fpolypeptides, proteins, and/or protein complexes of the invention areprovided in a form in which is they comprise more than about 10%, 20%,50%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 99.9% of the totalprotein in the final composition. In some embodiments the RSV Fpolypeptides, proteins, and/or protein complexes of the invention may beisolated and purified from other proteins, or any other undesirableproducts (such as non-cross-linked or non-pre-F RSV F), by standardmethods including, but not limited to, chromatography, glycerolgradients, affinity chromatography, centrifugation, ion exchangechromatography, size exclusion chromatography, and affinitychromatography, or by any other standard technique for the purificationof proteins known in the art. The RSV F polypeptides, proteins, and/orprotein complexes to be isolated may be expressed in high or low ionicmedia, or isolated in high or low ionic buffers or solutions. The RSV Fpolypeptides, proteins, and/or protein complexes of the invention mayalso be isolated at one or more temperatures that favor preservation ofthe desired conformation. They may also be isolated over a period oftime that diminishes the degree to which a preparation would have lostthe desired conformation. The degree to which a preparation of proteinsretains one or more desired conformations (such as the pre-Fconformation and/or conformations that favor binding to neutralizingantibodies, or ther desired properties) may be assayed by any suitablemethod known in the art, including, for example, but not limited to,biochemical, biophysical, immunologic, and virologic analyses. Suchassays include, for example, but are not limited to, immunoprecipation,enzyme-linked immunosorbent assays (ELISAs), or enzyme-linkedimmunosorbent spot (ELISPOT) assays, crystallographic analysis(including co-crystallization with antibodies), sedimentation,analytical ultracentrifugation, dynamic light scattering (DLS), electronmicroscopy (EM), cryo-EM tomography, calorimetry, surface plasmonresonance (SPR), fluorescence resonance energy transfer (FRET), circulardichroism analysis, and small angle x-ray scattering, neutralizationassays, antibody-dependent cellular cytotoxicity assays, and/orvirologic challenge studies in vivo.

The yield of the RSV F polypeptides, proteins, and/or protein complexesof the invention can be determined by any means known in the art, forexample, by comparing the amount of the final engineered proteins (suchas cross-linked pre-F RSV) as compared to the amount of the startingmaterial, or as compared to the amount of the materials present in anypreceding step of the production methods. Protein concentrations candetermined by standard procedures, such as, for example, Bradford orLowrie protein assays. The Bradford assay is compatible with reducingagents and denaturing agents (Bradford, M, 1976. Anal. Biochem. 72:248). The Lowry assay has better compatibility with detergents and thereaction is more linear with respect to protein concentrations andread-out (Lowry, O J, 1951. Biol. Chem. 193: 265).

Exemplary Production Methods

In some embodiments the present invention provides a method forproducing a RSV F protein stabilized in its pre-fusion conformation, themethod comprising: (a) obtaining an RSV F protein in its pre-Fconformation, (b) identifying one or more regions in the tertiary and/orquaternary structure of the RSV prefusion F protein in which theintroduction of one or more cross-links could stabilize the pre-Fconformation, and (c) introducing into the RSV prefusion F protein oneor more cross-links at one or more of the regions identified in step (b)to form an engineered RSV F protein locked in its pre-fusionconformation. In some embodiments, the regions identified in step (b)comprise one or more of the specific regions or specific amino acidresidues described herein. In some embodiments the cross-links aretargeted cross-links. In some embodiments the cross-links are targetedDT cross-links. In some embodiments the cross-links are stable underphysiological conditions. In some embodiments, the engineered RSV Fprotein stabilized in its pre-fusion conformation is useful as a vaccineimmunogen. In some embodiments, the engineered RSV F protein locked inits pre-fusion conformation has one or more of the following properties:(i) enhanced ability bind to a neutralizing antibody as compared to theRSV F protein not so engineered (i.e. as compared to the RSV F proteinwithout or before introduction of the cross-links), (ii) enhancedability bind to a broadly neutralizing antibody as compared to the RSV Fprotein not so engineered, (iii) enhanced ability bind to and activate Bcell receptors as compared to the RSV F protein not so engineered, (iv)enhanced ability to elicit an antibody response in an animal as comparedto the RSV F protein not so engineered, (v) enhanced ability to elicit aprotective antibody response in an animal as compared to the RSV Fprotein not so engineered, (vi) enhanced ability to elicit production ofneutralizing antibodies in an animal as compared to the RSV F proteinnot so engineered, (vii) enhanced ability to elicit production ofbroadly neutralizing antibodies in an animal as compared to the RSV Fprotein not so engineered, (viii) enhanced ability to elicit aprotective immune response in an animal as compared to the RSV F proteinnot so engineered, and (ix) enhanced ability to bind to and elicitproduction of antibodies that recognize quaternary neutralizing epitopesin an animal as compared to the RSV F protein not so engineered. In someembodiments the methods for producing an RSV F protein stabilized in itspre-fusion conformation described herein also comprise performing anassay to determine if the engineered RSV F protein stabilized in itspre-fusion conformation and/or has one or more of the properties listedabove.

Properties of RSV F Polypeptides, Proteins and/or Protein Complexes

In some embodiments, the RSV F polypeptides, proteins and/or proteincomplexes of the invention, including in particular those that arecross-linked as described herein, have certain structural, physical,functional, and/or biological properties. Such properties may includeone or more of the following, or any combination of the following:existence of the pre-F conformation, stability of the RSV pre-Fconformation; Improved stability of the RSV pre-F conformation (ascompared to non-cross-linked RSV F proteins); Improved half-life of theRSV pre-F conformation (as compared to non-cross-linked RSV F proteins);Improved thermostability (as compared to non-cross-linked RSV Fproteins); Prolonged shelf-life (as compared to non-cross-linked RSV Fproteins); Prolonged half-life inside the body of a subject (as comparedto non-cross-linked RSV F proteins); Ability to be stored in solutionwithout forming aggregates (including when present at a highconcentration in solution); Reduced aggregation in solution (as comparedto non-cross-linked RSV F proteins); Binding to an antibody; Binding toa neutralizing antibody; Binding to a broadly neutralizing antibody;Binding to a pre-F-specific antibody; Binding to an antibody thatrecognizes site ø; Binding to a conformationally-specific antibody;Binding to an antibody that recognizes a metastable epitope; Binding toan antibody selected from the group consisting of D25, AM22 and 5C4(which antibodies are described in McLellan et al., 2013, Science, 340,p. 1113; Kwakkenbos et al., 2010, Nature Medicine, 16, p. 123; Spits &Beaumont, U.S. patent application Ser. No. 12/600,950; Beaumont, Bakker& Yasuda, U.S. patent application Ser. No. 12/898,325, the contents ofeach of which are hereby incorporated by reference in their entireties);Binding to palivizumab (Synagis); Binding to the neutralizing antibody101F; Binding to a B cell receptor; Activation of a B Cell receptor;Eliciting an antibody response in an animal; Eliciting a protectiveantibody response in an animal; Eliciting production of neutralizingantibodies in an animal; Eliciting production of broadly neutralizingantibodies in an animal; Eliciting production of antibodies thatrecognize quaternary neutralizing epitopes (QNEs) in an animal;Eliciting a protective immune response in an animal; and/or Eliciting ahumoral immune response in an animal. In the case of binding to antibodymolecules, in some embodiments the RSV F polypeptides, proteins, and/orprotein complexes of the invention bind to the antibodies (such aspre-F-specific antibodies, antibodies that bind to site ø, and/or D25,AM22 or 5C4) with high specificity and/or with high affinity.

Assays for Properties

In some embodiments the RSV F polypeptides, proteins, and/or proteincomplexes of the invention, or any intermediates in their manufacture,may be analyzed to confirm that they have desired properties, such asthe desired structural, physical, functional, and/or biologicalproperties—such as those properties listed above or identified elsewherein this patent specification. For example, in some embodiments in vitroor in vivo assays can be performed to assess the RSV F protein'sconformational structure, stability (e.g. thermostability), half-life(e.g. inside the body of a subject), aggregation in solution, binding toan antibody (such as a neutralizing antibody, broadly neutralizingantibody; pre-F-specific antibody; antibody that recognizes site ø,conformationally-specific antibody, antibody that recognizes ametastable epitope, D25, AM22, 5C4, 101F or palivizumab), binding to a Bcell receptor, activation of a B Cell receptor, antigenicity,immunogenicity, ability to elicit an antibody response, ability toelicit a protective antibody/immune response, ability to elicitproduction of neutralizing antibodies, or ability to elicit a productionof broadly neutralizing antibodies. In embodiments where the RSV Fpolypeptides, proteins, and/or protein complexes of the invention aretested in an animal in vivo, the animal may be any suitable animalspecies, including, but not limited to a mammal (such as a rodentspecies (e.g. a mouse or rat), a rabbit, a ferret, a porcine species, abovine species, an equine species, an ovine species, or a primatespecies (e.g. a human or a non-human primate), or an avian species (suchas a chicken).

Assays for assessing a protein's conformational structure are well knownin the art and any suitable assay can be used, including, but notlimited to, crystallographic analysis (e.g. X-ray crystallography orelectron crystallography), sedimentation analysis, analyticalultracentrifugation, electron microscopy (EM), cryo-electron microscopy(cryo-EM), cryo-EM tomography, nuclear magnetic resonance (NMR), smallangle x-ray scattering, fluorescence resonance energy transfer (FRET)assays, and the like.

Assays for assessing a protein's stability are well known in the art andany suitable assay can be used, including, but not limited to,denaturing and non-denaturing electrophoresis, isothermal titrationcalorimetry, and time-course experiments in which proteins are incubatedand analyzed over time at varying protein concentrations, temperatures,pHs or redox conditions. Proteins may also be analyzed forsusceptibility to proteolytic degradation.

Assays for assessing binding of proteins to antibodies are well known inthe art, and any suitable assay can be used, including, but not limitedto, immunoprecipation assays, enzyme-linked immunosorbent assays(ELISAs), enzyme-linked immunosorbent spot assays (ELISPOTs),crystallographic assays (including co-crystallization with antibodies),surface plasmon resonance (SPR) assays, fluorescence resonance energytransfer (FRET) assays, and the like.

Assays for assessing neutralization activity are well known in the art,and any suitable assay can be used. For example, assays can be performedto determine the neutralizing activity of antibodies or antiseragenerated by vaccination/immunization of animals with the RSV Fpolypeptides, proteins, and/or protein complexes of the invention.Neutralization assays known in the art include, but are not limited to,those described by Dey et al. 2007 (Dey et al., 2007, Characterizationof Human Immunodeficiency Virus Type 1 Monomeric and Trimeric gp120Glycoproteins Stabilized in the CD4-Bound State: Antigenicity,Biophysics, and Immunogenicity. J Virol 81(11): 5579-5593) and Beddowset al., 2006 (Beddows et al., 2007, A comparative immunogenicity studyin rabbits of disulfide-stabilized proteolytically cleaved, solubletrimeric human immunodeficiency virus type 1 gp140, trimericcleavage-defective gp140 and momomeric gp120. Virol 360: 329-340).

Assays for assessing whether a vaccine immunogen is capable of elicitingan immune response and/or proving protective immunity are well known inthe art, and any suitable assay can be used. For example, assays can beperformed to determine whether vaccination/immunization of animals withthe RSV F polypeptides, proteins, and/or protein complexes of theinvention provide an immune response and/or protective immunity againstinfection with RSV. In some embodiments comparisons may be made betweenplacebo and test vaccinated groups with regard to their rates ofinfection or sero-conversion or viral loads.

Assays for assessing a protein's pharmacokinetics and bio-distributionare also well known in the art, and any suitable assay can be used toassess these properties of the RSV F polypeptides, proteins, and/orprotein complexes of the invention.

Compositions

In some embodiments the present invention provides compositionscomprising any of the RSV F polypeptides, proteins, and/or proteincomplexes described herein. In some embodiments such compositions may beimmunogenic compositions, vaccine compositions and/or therapeuticcompositions. In some embodiments, such compositions may be administeredto subjects.

In some embodiments the RSV F polypeptides, proteins, and/or proteincomplexes of the invention may be provided in a composition thatcomprises one or more additional active components, such as one or moreadditional vaccine immunogens or therapeutic agents. In some embodimentsthe RSV F polypeptides, proteins, and/or protein complexes of theinvention may be provided in a composition that comprises one or moreother components, including, but not limited to, pharmaceuticallyacceptable carriers, adjuvants, wetting or emulsifying agents, pHbuffering agents, preservatives, and/or any other components suitablefor the intended use of the compositions. Such compositions can take theform of solutions, suspensions, emulsions and the like. The term“pharmaceutically acceptable carrier” includes various diluents,excipients and/or vehicles in which, or with which, the RSV Fpolypeptides, proteins, and/or protein complexes of the invention can beprovided. The term “pharmaceutically acceptable carrier” includes, butis not limited to, carriers known to be safe for delivery to humanand/or other animal subjects, and/or approved by a regulatory agency ofthe Federal or a state government, and/or listed in the U.S.Pharmacopeia, and/or other generally recognized pharmacopeia, and/orreceiving specific or individual approval from one or more generallyrecognized regulatory agencies for use in humans and/or other animals.Such pharmaceutically acceptable carriers, include, but are not limitedto, water, aqueous solutions (such as saline solutions, buffers, and thelike), organic solvents (such as certain alcohols and oils, includingthose of petroleum, animal, vegetable or synthetic origin, such aspeanut oil, soybean oil, mineral oil, sesame oil), and the like. In someembodiments the compositions of the invention also comprise one or moreadjuvants. Exemplary adjuvants include, but are not limited to,inorganic or organic adjuvants, oil-based adjuvants, virosomes,liposomes, lipopolysaccharide (LPS), molecular cages for antigens (suchas immune-stimulating complexes (“ISCOMS”)), Ag-modifiedsaponin/cholesterol micelles that form stable cage-like structures thatare transported to the draining lymph nodes), components of bacterialcell walls, endocytosed nucleic acids (such as double-stranded RNA(dsRNA), single-stranded DNA (ssDNA), and unmethylated CpGdinucleotide-containing DNA), AUM, aluminum phosphate, aluminumhydroxide, and Squalene. In some embodiments virosomes are used as theadjuvant. Additional commercially available adjuvants that can be usedin accordance with the present invention include, but are not limitedto, the Ribi Adjuvant System (RAS, an oil-in-water emulsion containingdetoxified endotoxin (MPL) and mycobacterial cell wall components in 2%squalene (Sigma M6536)), TiterMax (a stable, metabolizable water-in-oiladjuvant (CytRx Corporation 150 Technology Parkway TechnologyPark/Atlanta Norcross, Ga. 30092)), Syntex Adjuvant Formulation (SAF, anoil-in-water emulsion stabilized by Tween 80 and pluronicpolyoxyethlene/polyoxypropylene block copolymer L121 (ChironCorporation, Emeryville, Calif.)), Freund's Complete Adjuvant, Freund'sIncomplete Adjuvant, ALUM—aluminum hydroxide, Al(OH)3 (available asAlhydrogel, Accurate Chemical & Scientific Co, Westbury, N.Y.),SuperCarrier (Syntex Research 3401 Hillview Ave. P.O. Box 10850 PaloAlto, Calif. 94303), Elvax 40W1,2(an ethylene-vinyl acetate copolymer(DuPont Chemical Co. Wilmington, Del.)), L-tyrosine co-precipitated withthe antigen (available from numerous chemical companies); Montanide (amanide-oleate, ISA Seppic Fairfield, N.J.)), AdjuPrime (a carbohydratepolymer), Nitrocellulose-absorbed protein, Gerbu adjuvant (C-C Biotech,Poway, Calif.), and the like.

In some embodiments the compositions of the invention comprise an“effective amount” of a RSV F polypeptide, protein, and/or proteincomplex of the invention. An “effective amount” is an amount required toachieve a desired end result. Examples of desired end results include,but are not limited to, the generation of a humoral immune response, thegeneration of a neutralizing antibody response, the generation of abroadly neutralizing antibody response, and the generation of protectiveimmunity. The amount of a RSV F polypeptide, protein, and/or proteincomplex of the invention that is effective to achieve the desired endresult will depend on variety of factors including, but not limited to,the type, subtype, and strain of the RSV virus against which protectionor some other therapeutic effect is sought, the species of the intendedsubject (e.g. whether a human or some other animal species), the ageand/or sex of the intended subject, the planned route of administration,the planned dosing regimen, the seriousness of any ongoing influenzainfection (e.g. in the case of therapeutic uses), and the like. Theeffective amount—which may be a range of effective amounts—can bedetermined by standard techniques without any undue experimentation, forexample using in vitro assays and/or in vivo assays in the intendedsubject species or any suitable animal model species. Suitable assaysinclude, but are not limited to, those that involve extrapolation fromdose-response curves and/or other data derived from in vitro and/or invivo model systems. In some embodiments the effective amount may bedetermined according to the judgment of a medical or veterinarypractitioner based on the specific circumstances.

Uses of the RSV F Polypeptides, Proteins & Protein Complexes of theInvention

In some embodiments, the RSV F polypeptides, proteins, and proteincomplexes of the invention may be useful as research tools, asdiagnostic tools, as therapeutic agents, as targets for the productionof antibody reagents or therapeutic antibodies, and/or as vaccines orcomponents of vaccine compositions. For example, in some embodiments theRSV F polypeptides, proteins, and protein complexes of the invention areuseful as a vaccine immunogens in animal subjects, such as mammaliansubject, including humans. These and other uses of the RSV Fpolypeptides, proteins, and protein complexes of the invention aredescribed more fully below. Those of skill in the art will appreciatethat the RSV F polypeptides, proteins, and protein complexes of theinvention may be useful for a variety of other applications also, andall such applications and uses are intended to fall within the scope ofthis invention.

Tools for Studying RSV F Antibodies

In one embodiment, the RSV F polypeptides, proteins, and proteincomplexes of the invention may be useful as analytes for assaying and/ormeasuring binding of, and/or titers of, anti-RSV F antibodies, forexample in ELISA assays, Biacore/SPR binding assays, and/or any otherassays for antibody binding known in the art. For example, the RSV Fpolypeptides, proteins, and protein complexes of the invention could beused to analyze, and/or compare the efficacy of anti-RSV F antibodies.

Tools for Generation of Antibodies

The RSV F polypeptides, proteins, and protein complexes of the inventionmay also be useful for the generation of therapeutic antibodies and/orantibodies that can be used as research tools or for any other desireduse. For example, the RSV F polypeptides, proteins, and proteincomplexes of the invention can be used for immunizations to obtainantibodies to the RSV F protein for use as research tools and/or astherapeutics. In some embodiments the RSV F polypeptides, proteins, andprotein complexes of the invention can be used to immunize a non-humananimal, such as a vertebrate, including, but not limited to, a mouse,rat, guinea pig, rabbit, goat, non-human primate, etc. in order togenerate antibodies. Such antibodies, which may be monoclonal orpolyclonal, and/or cells that produce such antibodies, can then beobtained from the animal. For example, in some embodiments RSV Fpolypeptides, proteins, and protein complexes of the invention may beused to immunize a mouse and to produce and obtain monoclonalantibodies, and/or hybridomas that produce such monoclonal antibodies.Such methods can be carried out using standard methods known in the artfor the production of mouse monoclonal antibodies, including standardmethods for hybridoma production. In some embodiments RSV Fpolypeptides, proteins, and protein complexes of the invention may beused for the production of a chimeric (e.g. part-human), humanized, orfully-human antibody, for example using any of the methods currentlyknown in the art for production of chimeric, humanized and fully humanantibodies, including, but not limited to, CDR grafting methods,phage-display methods, transgenic mouse methods (e.g. using a mouse thathas been genetically altered to allow for the production of fully humanantibodies, such as the Xenomouse) and/or any other suitable methodknown in the art. Antibodies to the RSV F polypeptides, proteins, andprotein complexes of the invention made using such systems can becharacterized antigenically using one or a set of several antigens,preferably including the RSV F polypeptides, proteins, and proteincomplexes of the invention themselves. Additional characterization ofsuch antibodies may be carried out by any standard methods known to oneof ordinary skill in the art, including, but not limited to, ELISA-basedmethods, SPR-based methods, biochemical methods (such as, but notlimited to, iso-electric point determination), and methods known in theart for studying biodistribution, safety, and efficacy of antibodies—forexample in preclinical and clinical studies.

Administration to Subjects

In some embodiments, the present invention provides methods thatcomprise administering the RSV F polypeptides, proteins and/or proteincomplexes of the invention (or compositions comprising such RSV Fpolypeptides, proteins and/or protein complexes) to subjects. Suchmethods may comprise methods for treating individuals having RSV (i.e.therapeutic methods) and/or methods for protecting individuals againstfuture RSV infection (i.e. prophylactic methods).

Subjects to which the RSV F polypeptides, proteins and/or proteincomplexes of the invention, or compositions comprising such RSV Fpolypeptides, proteins and/or protein complexes, can be administered(for example in the course of a method of treatment or a method ofvaccination) include any and all animal species, including, inparticular, those that are susceptible to RSV infection or that canprovide model animal systems for the study of RSV infection. In someembodiments, the subjects are mammalian species. In some embodiments,the subjects are avian species. Mammalian subjects include, but are notlimited to, humans, non-human primates, rodents, rabbits, and ferrets.Avian subjects include, but are not limited to chickens, such as thoseon poultry farms. In some embodiments the subjects to which the RSV Fpolypeptides, proteins and/or protein complexes of the invention, orcompositions comprising such RSV F polypeptides, proteins and/or proteincomplexes are administered, either have RSV, or are at risk of RSVinfection. In some embodiments, the subjects are immuno-compromised. Insome embodiments, the subjects have a heart disease or disorder. In someembodiments, the subject is a human of greater than about 50 years inage, greater than about 55 years in age, greater than about 60 years inage, greater than about 65 years in age, greater than about 70 years inage, greater than about 75 years in age, greater than about 80 years inage, greater than about 85 years in age, or greater than about 90 yearsin age. In some embodiments, the subject is a human of less than about 1month in age, less than about 2 months in age, less than about 3 monthsin age, less than about 4 months in age, less than about 5 months inage, less than about 6 months in age, less than about 7 months in age,less than about 8 months in age, less than about 9 months in age, lessthan about 10 months in age, less than about 11 months in age, less thanabout 12 months in age, less than about 13 months in age, less thanabout 14 months in age, less than about 15 months in age, less thanabout 16 months in age, less than about 17 months in age, less thanabout 18 months in age, less than about 19 months in age, less thanabout 20 months in age, less than about 21 months in age, less thanabout 22 months in age, less than about 23 months in age, or less thanabout 24 months in age.

Various delivery systems are known in the art and any suitable deliverysystems can be used to administer the compositions of the presentinvention to subjects. Such delivery systems include, but are notlimited to, intradermal, intramuscular, intraperitoneal, intravenous,subcutaneous, intranasal, epidural, and oral delivery systems. Thecompositions of the present invention may be administered by anyconvenient route, for example by infusion or bolus injection, byabsorption through epithelial or mucocutaneous linings (e.g., oralmucosa, rectal and intestinal mucosa, etc.) and may be administeredtogether with other biologically active agents. Administration can besystemic or local. Pulmonary administration can also be employed, e.g.,by use of an inhaler or nebulizer, and formulation with an aerosolizingagent.

In some embodiments it may be desirable to administer the pharmaceuticalcompositions of the invention locally to a tissue in which the RSV Fprotein or polypeptide may be most effective in generating a desirableoutcome. This may be achieved by, for example, local infusion,injection, delivery using a catheter, or by means of an implant, such asa porous, non-porous, or gelatinous implant or an implant comprising oneor more membranes (such as sialastic membranes) or fibers from orthrough which the protein or protein complexes may be released locally.In some embodiments a controlled release system may be used. In someembodiments a pump may be used (see Langer, supra; Sefton, 1987. CRCCrit. Ref. Biomed. Eng. 14: 201; Buchwald et al., 1980. Surgery 88: 507;Saudek et al., 1989. N. Engl. J. Med. 321: 574). In some embodimentspolymeric materials may be used to facilitate and/or control release ofthe RSV prefusion F protein of the invention (see Medical Applicationsof Controlled Release, Langer and Wise (eds.), 1974. CRC Pres., BocaRaton, Fla.; Controlled Drug Bioavailability, 1984. Drug Product Designand Performance, Smolen and Ball (eds.), Wiley, New York; Ranger &Peppas, 1983 Macromol. Sci. Rev. Macromol. Chem. 23: 61; see also Levyet al., 1985. Science 228:190; During et al, 1989. Ann. Neurol. 25: 351;Howard et al., 1989. J. Neurosurg 71:105). In some embodiments acontrolled release system can be placed in proximity to the tissue/organto which the RSV prefusion F protein or polypeptide is to be delivered(see, e.g., Goodson, 1984. Medical Applications of Controlled Release,supra, vol. 2: 115-138). Some suitable controlled release systems thatmay be used in conjunction with the present invention are describedLanger, 1990, Science; vol. 249: pp. 527-1533

In some embodiments, administration of the compositions of the inventioncan be performed in conjunction with administration of one or moreimmunostimulatory agents. Non-limiting examples of suchimmunostimulatory agents include various cytokines, lymphokines andchemokines with immunostimulatory, immunopotentiating, andpro-inflammatory activities, such as interleukins (e.g., IL-1, IL-2,IL-3, IL-4, IL-12, IL-13); growth factors (e.g., granulocyte-macrophage(GM)-colony stimulating factor (CSF)); and other immunostimulatoryagents, such as macrophage inflammatory factor, Flt3 ligand, B7.1; B7.2.The immunostimulatory agents can be administered in the same formulationas the RSV F protein or polypeptide, or can be administered separately.

In some embodiments, the RSV F polypeptides, proteins, and/or proteincomplexes of the invention, or compositions comprising them, can beadministered to subjects in a variety of different RSV vaccinationmethods or regimens. In some such embodiments, administration of asingle dose is preferred. However, in other embodiments, additionaldosages can be administered, by the same or different route, to achievethe desired prophylactic effect. In neonates and infants, for example,multiple administrations may be required to elicit sufficient levels ofimmunity. Administration can continue at intervals throughout childhood,as necessary to maintain sufficient levels of protection against RSVinfection. Similarly, adults who are particularly susceptible to RSVinfection, such as, for example, the elderly and immunocompromisedindividuals, may require multiple immunizations to establish and/ormaintain protective immune responses. Levels of induced immunity can bemonitored, for example, by measuring amounts of neutralizing secretoryand serum antibodies, and dosages adjusted or vaccinations repeated asnecessary to elicit and maintain desired levels of protection.

In some embodiments, dosing regimens may comprise a singleadministration/immunization. In other embodiments, dosing regimens maycomprise multiple administrations/immunizations. For example, vaccinesmay be given as a primary immunization followed by one or more boosters.In some embodiments of the present invention such a “prime-boost”vaccination regimen may be used. For example, in some such prime-boostregimens a composition comprising a RSV F polypeptide, protein orprotein complex as described herein may be administered to an individualon multiple occasions (such as two, three, or even more occasions)separated in time, with the first administration being the “priming”administration and subsequent administrations being “booster”administrations. In other such prime-boost regimens a compositioncomprising a RSV F polypeptide, protein or protein complex as describedherein may be administered to an individual after first administering tothe individual a composition comprising a viral or DNA vector encodingan RSV polypeptide, protein or protein complex as a “priming”administration, with one or more subsequent “booster” administrations ofa composition comprising a RSV F polypeptide, protein or protein complexas described herein. Boosters may be delivered via the same and/ordifferent route as the primary immunization. Boosters are generallyadministered after a time period after the primary immunization or thepreviously administered booster. For example, a booster can be givenabout two weeks or more after a primary immunization, and/or a secondbooster can be given about two weeks or more after the first boosters.Boosters may be given repeatedly at time periods, for example, about twoweeks or greater throughout up through the entirety of a subject's life.Boosters may be spaced, for example, about two weeks, about three weeks,about four weeks, about one month, about two months, about three months,about four months, about five months, about six months, about sevenmonths, about eight months, about nine months, about ten months, abouteleven months, about one year, about one and a half years, about twoyears, about two and a half years, about three years, about three and ahalf years, about four years, about four and a half years, about fiveyears, or more after a primary immunization or after a previous booster.

Preferred unit dosage formulations are those containing a dose or unit(e.g. an effective amount), or an appropriate fraction thereof, of theRSV F polypeptides, proteins, and/or protein complexes of the invention.In addition to such ingredients, formulations of the present inventionmay include other agents commonly used by one of ordinary skill in theart. Pharmaceutical compositions provided by the invention may beconveniently presented in preferred unit dosage formulations preparedusing conventional pharmaceutical techniques. Such techniques includethe step of bringing into association the active ingredient and thepharmaceutical carrier(s) or excipient(s) or other ingredients. Ingeneral, the formulations are prepared by uniformly and intimatelybringing into association the active ingredient with liquid carriers.Formulations suitable for parenteral administration include aqueous andnon-aqueous sterile injection solutions which may contain anti-oxidants,buffers, bacteriostats and solutes which render the formulation isotonicwith the blood of the intended recipient, and aqueous and non-aqueoussterile suspensions which may include suspending agents and thickeningagents. The formulations may be presented in unit-dose or multi-dosecontainers, for example, sealed ampoules and vials, and may be stored ina freeze-dried (lyophilized) condition requiring only the addition ofthe sterile liquid carrier, for example, water for injections,immediately prior to use. Extemporaneous injection solutions andsuspensions may be prepared from sterile powders, granules and tabletscommonly used by one of ordinary skill in the art.

Kits

The present invention further provides kits comprising RSV polypeptides,proteins or protein complexes of the invention, or compositionscontaining such polypeptides, proteins or protein complexes. Tofacilitate use of the methods and compositions of the invention, any ofthe components and/or compositions described herein, and additionalcomponents useful for experimental or therapeutic or vaccine purposes,can be packaged in the form of a kit. Typically, the kit contains, inaddition to the above components, additional materials which caninclude, e.g., instructions for using the components, packagingmaterial, a container, and/or a delivery device.

Various embodiments of the present invention may also be furtherdescribed by the following non-limiting examples:

Example

RSV F protein variants E222Y (SEQ ID NO:13), K226Y (SEQ ID NO:15), V469Y(SEQ ID NO:16), N88Y/S255Y (SEQ ID NO:18), V185Y/K427Y (SEQ ID NO:20)were expressed in human cells as modified by the introduction ofdi-tyrosine bonds as described below.

Expression Plasmids. cDNA encoding a C-terminal fusion of the WT humanRSV-F ectodomain or DS-Cav1 protein ectodomain to the T4 fibritin foldontrimerization motif, thrombin cleavage-site, 6× HIS-tag (SEQ ID NO: 46),and strep-tag were codon-optimized for human expression and synthesized(Geneart). cDNA encoding RSV F protein variants E222Y (SEQ ID NO:13),K226Y (SEQ ID NO:15), V469Y (SEQ ID NO:16), N88Y/S255Y (SEQ ID NO:18),V185Y/K427Y (SEQ ID NO:20) were also synthesized. These DNA sequenceswere cloned into the pCDNA3.1/zeo+ expression vector (Invitrogen) via 5′BamHI and 3′XhoI restriction endonuclease sites using standard methods(FIG. 33).

Cells and Transfections. HEK 293 cells (ATCC) were grown in Dulbecco'sModification of Eagle's Medium (DMEM, Invitrogen) supplemented with 10%Fetal Bovine Serum and 50 μg/ml gentamycin. Cells were seeded into6-well tissue culture plates (Corning) and grown till 80% confluent (˜24h). Cells were transfected with 2 μg of each RSV-F expression plasmidper well using a 1:4 ratio (MN) of DNA to polyethylenimine (25 kDa,linear). 16 h post-transfection, media was removed and replaced with 2ml/well of serum-free Freestyle-293 expression media (Invitrogen). Cellswere cultured at 37 degrees C. for an additional 48 h-72 h in 5% CO₂prior to collection and analysis.

Detection of RSV-F in Cell Supernatants by ELISA. After collection,total RSV-F protein was directly captured from cell supernatants for 1 hat room temperature in EIA/RIA high-bind 96-well plates (Corning).Protein-containing and control wells were subsequently blocked with 4%nonfat milk in PBS-tween20 (0.05%) for 1 h at room temperature. Plateswere washed 3× with PBS-T (400 μl/well). Total RSV-F was detected for 1h using a high-affinity human anti-hRSV antibody (100 ng/ml in PBS) thatrecognizes both pre- and post-fusion forms of RSV-F. Prefusion F wasdetected using a pre-F specific human monoclonal antibody (2 μg/ml inPBS) that recognizes site ø. Wells were again washed 3× in PBS-Tfollowed by a 1 h room temperature incubation with an HRP-conjugatedgoat anti-human F(ab)₂ (Jackson Immunoresearch) at a 1:5000 dilution inPBS. Wells were washed 6× with PBS-T and total RSV-F was detected andquantified using 100 μl 3,3′,5,5′-tetramethylbenzidine (TMB) to producea colorimetric signal. The colorimetric reaction was stopped by theaddition of equal volume 4N sulfuric acid. Final Optical Densityreadings were taking at 450 nm using a BioRad Benchmark Plus microplateabsorbance spectrophotometer. A 2× serial dilution series for eachsupernatant was used to determine the linear range of detectable signalfor each sample allowing accurate comparison of the relative amount ofRSV-F between samples (FIG. 35).

Di-tyrosine-Cross-linking in Cell Supernatants. Immediately followingcollection, 100 μl of transfected and control cell supernatants weretransferred to wells of black, flat-bottom, non-binding 96-well FIAplates (Greiner bio-one). 300 ng of Arthromyces ramosus peroxidase wasadded to each sample to be cross-linked. 1 μl of 1.2 mM H₂O₂ was thenadded to both control and DT reactions for a final reactionconcentration of 120 μM H₂O₂. Reactions were allowed to proceed for 20minutes at room temperature followed by alkalization of the reactions byaddition of equal volume sodium phosphate buffer at pH 10. Di-tyrosinespecific fluorescence was read at an excitation wavelength of 320 nm andemission wavelength of 405 nm using a Thermo Scientific FluoroskanAscent FL (FIG. 34).

72 h post transfection, supernatents were cross-linked (DT) or leftuncross-linked and total protein was measured by ELISA using ahigh-affinity human anti-hRSV antibody (100 ng/ml in PBS) thatrecognizes both pre- and post-fusion forms of RSV-F. See FIG. 35A.Following storage at 4 degrees C. for 16 days presentation of site ø wasmeasured by ELISA using a preF specific human monoclonal antibody (2μg/ml in PBS) that recognizes site ø. Di-tyrosine cross-links were foundto stabilize key epitope on RSV prefusion F protein. See FIG. 35B.

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. The invention may also be further defined in terms of thefollowing claims.

1. A RSV F polypeptide, protein or protein complex comprising an aminoacid sequence having at least 70% sequence identity to amino acidresidues 1-513 of SEQ ID NO.1 (RSV type A) or amino acid residues 1-513of SEQ ID NO.3 (RSV type B), wherein the amino acid sequence comprises apoint mutation to tyrosine at one or more of amino acid positions 77,88, 97, 147, 150, 155, 159, 183, 185, 187, 220, 222, 223, 226, 255, 427or
 469. 2. A RSV F polypeptide, protein or protein complex according toclaim 1, wherein the polypeptide, protein or protein complex is foldedinto the pre-F conformation and comprises at least one di-tyrosinecross-link, wherein one or both tyrosines of the at least one cross-linkoriginate from a point mutation to tyrosine, and wherein the cross-linksare located between one or more paired tyrosine amino acid residueslocated at amino acid positions: 147 and 286; 198 and 220; 198 and 222;198 and 223; 198 and 226; 33 and 469; 77 and 222; 88 and 255; 97 and159; 183 and 427; 185 and 427; 88 and 255; or 187 and
 427. 3. A RSV Fpolypeptide, protein or protein complex comprising according to claim 1,comprising amino acid residues 1-513 of sequence of SEQ ID NO. 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31 or
 32. 4. A RSV Fpolypeptide, protein or protein complex according to claim 1, whereinthe polypeptide, protein or protein complex is capable of folding intothe pre-F conformation.
 5. A RSV F polypeptide, protein or proteincomplex according to claim 1, wherein the polypeptide, protein orprotein complex further comprises one or more point mutations tocysteine.
 6. A RSV F polypeptide, protein or protein complex accordingto claim 1, wherein the polypeptide, protein or protein complex furthercomprises one or more cavity-filling hydrophobic amino acidsubstitutions.
 7. A RSV F polypeptide, protein or protein complexaccording to claim 1, wherein the polypeptide, protein or proteincomplex further comprises a trimerization domain.
 8. A RSV Fpolypeptide, protein or protein complex according to claim 7, whereinthe trimerization domain is a foldon domain.
 9. A RSV F polypeptide,protein or protein complex according to claim 1, wherein thepolypeptide, protein or protein complex is capable of elicitingproduction of RSV-specific antibodies in a subject.
 10. A RSV Fpolypeptide, protein or protein complex according to claim 1, whereinthe polypeptide, protein or protein complex is capable of binding to anantibody that recognizes antigenic site ø.
 11. A nucleic acid moleculeencoding a RSV F polypeptide, protein or protein complex according toclaim
 1. 12. A composition comprising a RSV F polypeptide, protein orprotein complex according to claim
 1. 13. The composition of claim 12,wherein the composition is a vaccine composition.
 14. The composition ofclaim 13, wherein the composition further comprises an adjuvant, acarrier, an immunostimulatory agent, or any combination thereof.
 15. Amethod of vaccinating a subject against RSV, the method comprisingadministering to a subject a composition comprising an effective amountof a RSV F polypeptide, protein or protein complex according to claim 1.16. The method of claim 15, wherein the subject is a human of less than24 months in age.
 17. The method of claim 15, wherein the subject is ahuman of greater than 50 years in age.
 18. The method of claim 15,wherein the administering comprises administering a single dosage of thecomposition.
 19. The method of claim 15, wherein the administeringcomprises administering a first “priming” dosage of the composition andone or more subsequent “boosting” dosages of the composition